diff --git a/bin/CodonCorrectionReferences/AnnotatableGenePositions.txt b/bin/CodonCorrectionReferences/AnnotatableGenePositions.txt
new file mode 100644
index 0000000..dadc983
--- /dev/null
+++ b/bin/CodonCorrectionReferences/AnnotatableGenePositions.txt
@@ -0,0 +1,1791 @@
+Sequence_name, gag_start, gag_end, pol_start, pol_end, vif_start, vif_end, vpr_start, vpr_end, vpu_start, vpu_end, env_start, env_end, nef_start, nef_end, 
+26_A5U.CD.02.02CD_KS069.FM877780, 295, 1779, 1740, 4583, 4528, 5106, 5046, 5339, 5552, 5797, 5715, 8297, 8299, 8937
+02_AG.CI.16.DEURF16CI022.MH078539, 103, 1593, 1563, 4409, 4351, 4929, 4869, 5159, 5377, 5622, 5540, 8140, 8142, 8774
+A2C.ZM.90.ZAM184.U86780, 169, 1653, 1614, 4457, 4402, 4980, 4920, 5210, 5432, 5677, 5595, 8141, 8143, 8766
+B.JP.04.DR6175.AB480694, 787, 2283, 2244, 5087, 5032, 5598, 5550, 5828, 6040, 6285, 6203, 8746, 8748, 9377
+GOR.CM.07.SIVgor2139_287.FJ424866, 351, 1820, 1790, 4654, 4578, 5156, 5096, 5392, 5611, 5850, 5774, 8383, 8385, 9017
+A1.KE.06.06KECst_005.FJ623481, 2, 1501, 1462, 4305, 4250, 4828, 4768, 5058, 5280, 5528, 5446, 8058, 8066, 8686
+C.ZA.00.1171MB.AY463232, 241, 1719, 1680, 4523, 4468, 5046, 4986, 5276, 5495, 5755, 5673, 8213, 8215, 8838
+C.BW.00.00BW3886_8.AF443112, 166, 1665, 1626, 4469, 4414, 4992, 4932, 5222, 5426, 5686, 5604, 8168, 8170, 8793
+F2.CM.11.DEMF211CM025.KU749420, 153, 1631, 1601, 4444, 4389, 4970, 4910, 5200, 5412, 5657, 5575, 8142, 8144, 8800
+A6.RU.13.ARH028.MH330337, 103, 1599, 1560, 4403, 4348, 4926, 4866, 5156, 5372, 5617, 5535, 8108, 8110, 8733
+A1D.TZ.97.TZBFL0086.AF442566, 137, 1633, 1594, 4437, 4382, 4960, 4900, 5190, 5412, 5657, 5575, 8136, 8138, 8758
+01_AE.CN.07.07CNYN317.KF835504, 175, 1665, 1626, 4469, 4414, 4977, 4932, 5210, 5419, 5664, 5582, 8137, 8139, 8756
+A1.UG.11.10203v01_01.MN791169, 1, 1497, 1458, 4301, 4246, 4824, 4764, 5054, 5270, 5515, 5433, 7982, 7984, 8598
+01_AE.PH.16.DE00116PH013.MH078562, 170, 1651, 1621, 4464, 4409, 4987, 4927, 5217, 5433, 5678, 5596, 8181, 8183, 8797
+A1D.UG.08.p191982.JX236675, 793, 2286, 2247, 5090, 5035, 5613, 5553, 5843, 6055, 6300, 6218, 8767, 8769, 9395
+B.US.07.HIV_US_BID_V3020_2007.JQ403059, 1, 1503, 1464, 4307, 4252, 4830, 4770, 5060, 5286, 5525, 5449, 8028, 8030, 8656
+02_AG.UG.10.DEURF10UG006.KF716488, 159, 1667, 1637, 4480, 4425, 5003, 4943, 5233, 5455, 5700, 5618, 8197, 8199, 8822
+A1CD.KE.05.05KE295198V5.KT022401, 2, 1495, 1456, 4299, 4244, 4822, 4762, 5052, 5261, 5521, 5439, 8000, 8002, 8625
+C.MW.09.DEMC09MW008.KP109525, 178, 1659, 1620, 4475, 4408, 4986, 4926, 5216, 5425, 5685, 5603, 8194, 8196, 8813
+B.US.x.CR0206U.FJ469705, 22, 1527, 1488, 4331, 4276, 4854, 4794, 5084, 5296, 5541, 5459, 8056, 8058, 8681
+02_AG.GW.14.DEURF14GW040.MN703132, 427, 1905, 1875, 4718, 4663, 5241, 5181, 5471, 5693, 5938, 5856, 8438, 8440, 9063
+01_AE.SE.12.069SE.MF373172, 1, 1497, 1458, 4301, 4246, 4824, 4764, 5054, 5270, 5515, 5433, 8015, 8017, 8637
+A1.SE.12.065SE.MF373168, 1, 1506, 1467, 4310, 4255, 4833, 4773, 5063, 5285, 5533, 5451, 8066, 8068, 8736
+A1.SE.93.001UG.MF373124, 1, 1500, 1461, 4304, 4249, 4827, 4767, 5060, 5282, 5524, 5442, 8048, 8050, 8664
+B.BR.05.05BR1104.JN692474, 246, 1748, 1709, 4552, 4497, 5075, 5015, 5305, 5517, 5762, 5680, 8244, 8246, 8869
+C.ZA.99.99ZALT45.EU293449, 792, 2270, 2231, 5074, 5019, 5597, 5537, 5827, 6036, 6296, 6214, 8781, 1, 618
+B.DE.08.147984.KT124751, 1, 1506, 1467, 4310, 4255, 4833, 4773, 5063, 5275, 5511, 5438, 8050, 8052, 8699
+B.US.18.5101_wk_2_5_G24.MW059247, 137, 1645, 1615, 4458, 4403, 4981, 4921, 5214, 5426, 5671, 5589, 8138, 8140, 8766
+CPZ.CD.06.BF1167.JQ866001, 799, 2385, 2355, 5198, 5143, 5733, 5673, 5960, 6151, 6396, 6344, 8998, 9001, 9588
+A6.UA.11.DEMA111UA002.KU749399, 372, 1868, 1829, 4672, 4617, 5195, 5135, 5422, 5638, 5883, 5801, 8356, 8358, 8981
+C.SE.11.063BI.MF373166, 1, 1494, 1455, 4298, 4243, 4821, 4761, 5051, 5270, 5515, 5442, 8063, 8065, 8706
+C.ZA.04.04ZASK234B1.DQ093605, 224, 1699, 1660, 4503, 4448, 5026, 4966, 5256, 5465, 5710, 5643, 8177, 8179, 8838
+33_01B.MY.05.05MYKL015_2.DQ366660, 174, 1661, 1631, 4474, 4419, 4997, 4937, 5230, 5446, 5691, 5609, 8173, 8175, 8789
+01_AE.TH.10.40094v09_03.MN792055, 1, 1485, 1446, 4352, 4297, 4872, 4815, 5111, 5327, 5572, 5490, 8144, 8146, 8766
+01A1F2.CM.07.BS72.KR017779, 263, 1747, 1717, 4560, 4505, 5083, 5023, 5313, 5529, 5774, 5692, 8247, 8249, 8899
+B.US.10.505_0695a.WG06.MG196787, 211, 1719, 1680, 4523, 4468, 5046, 4986, 5276, 5488, 5733, 5651, 8224, 8226, 8852
+B.DE.86.HAN.U43141, 259, 1758, 1719, 4562, 4507, 5085, 5025, 5315, 5527, 5772, 5690, 8257, 8259, 8861
+B.US.04.HIV_US_BID_V5261_2004.JQ403104, 16, 1530, 1491, 4334, 4279, 4857, 4797, 5087, 5299, 5544, 5462, 7984, 7986, 8624
+D.KE.97.ML415_2.AY322189, 256, 1758, 1719, 4562, 4507, 5085, 5025, 5315, 5528, 5773, 5691, 8267, 8269, 8913
+C.ZA.03.03ZASK006B2.AY878056, 225, 1739, 1700, 3835, 4488, 5066, 5006, 5296, 5511, 5771, 5689, 8247, 8249, 8887
+BC.BR.01.01_BR_RGS45.GQ365651, 328, 1845, 1806, 4649, 4594, 5172, 5112, 5402, 5621, 5881, 5799, 8378, 8380, 9018
+O.CM.95.LA29YBF26.KU168281, 842, 2338, 2308, 5181, 5096, 5674, 5614, 5916, 6122, 6379, 6297, 8912, 8914, 9561
+C.ZA.13.DEMC13ZA152.KU749417, 154, 1659, 1620, 4463, 4408, 4986, 4926, 5216, 5435, 5695, 5613, 8216, 8218, 8859
+B.US.x.CR0164U.FJ469702, 15, 1517, 1478, 4321, 4266, 4844, 4784, 5074, 5286, 5531, 5449, 8037, 8039, 8668
+F1.BR.01.01BRRJSB153.MG365763, 724, 2202, 2172, 5015, 4960, 5538, 5478, 5768, 5990, 6235, 6153, 8699, 8701, 9315
+27_cpx.CD.97.97CDKTB49.AJ404325, 1, 1500, 1461, 4304, 4249, 4827, 4767, 5057, 5278, 5523, 5441, 7999, 8001, 8624
+01_AE.TH.04.BKM.DQ314732, 751, 2244, 2205, 5060, 4993, 5571, 5511, 5801, 6017, 6271, 6189, 8804, 8806, 9420
+07_BC.CN.07.07CNYN323.KF835510, 156, 1655, 1616, 4459, 4404, 4985, 4925, 5215, 5427, 5672, 5590, 8160, 8162, 8788
+14_BG.PT.00.00PTHDE10.GU230137, 1, 1485, 1455, 4298, 4243, 4821, 4761, 5051, 5273, 5518, 5436, 8012, 8014, 8625
+B.US.18.5203_wk_2_4_B21.MW059684, 86, 1588, 1549, 4392, 4337, 4915, 4855, 5145, 5357, 5602, 5520, 8099, 8101, 8742
+B.BR.04.04BR1055.JN692454, 252, 1757, 1718, 4561, 4506, 5084, 5024, 5314, 5526, 5771, 5689, 8256, 8258, 8881
+28_BF1.BR.99.BREPM12609.DQ085873, 159, 1649, 1619, 4462, 4407, 4985, 4925, 5215, 5427, 5672, 5590, 8196, 8198, 8827
+C.ZA.03.03ZAPS091MB1.DQ275645, 224, 1693, 1654, 4497, 4442, 5020, 4960, 5250, 5463, 5717, 5641, 8154, 8156, 8779
+C.IN.14.NIRT004.KX069222, 1, 1473, 1434, 4277, 4222, 4800, 4740, 5030, 5239, 5493, 5411, 7969, 7971, 8594
+C.ZA.03.03ZAPS116MB1.DQ445635, 225, 1700, 1661, 4504, 4449, 5027, 4967, 5257, 5466, 5726, 5644, 8181, 8183, 8806
+A6.RU.12.BLG044.MH330354, 100, 1596, 1557, 4400, 4345, 4923, 4863, 5153, 5369, 5614, 5532, 8132, 8134, 8763
+C.ZM.09.Z331F_15Apr09_PL_NFLG_SGA22.KR820304, 210, 1691, 1652, 4495, 4440, 5027, 4958, 5248, 5467, 5727, 5645, 8323, 8325, 8951
+F1.ES.02.ES_X845_4.FJ670516, 248, 1735, 1705, 4548, 4493, 5071, 5011, 5301, 5523, 5768, 5686, 8214, 8216, 8833
+01_AE.CN.07.07CNYN337.KF835523, 174, 1682, 1652, 4495, 4440, 5018, 4958, 5248, 5464, 5709, 5627, 8275, 8277, 8921
+B.BR.09.DEMB09BR040.KU749389, 335, 1837, 1798, 4641, 4586, 5164, 5104, 5394, 5606, 5851, 5769, 8360, 8362, 8982
+09_cpx.SN.95.95SN7808.AY093604, 1, 1482, 1443, 4286, 4231, 4809, 4749, 5042, 5264, 5509, 5427, 7970, 7972, 8592
+02_AG.CI.16.DE00216CI019.MH078536, 163, 1641, 1611, 4454, 4399, 4977, 4917, 5207, 5427, 5672, 5590, 8136, 8138, 8758
+22_01A1.CM.10.LB013.JN864058, 30, 1517, 1487, 4330, 4275, 4853, 4793, 5083, 5299, 5544, 5462, 8059, 8061, 8675
+A1GHU.GA.x.VI354.AF076474, 159, 1643, 1613, 4456, 4401, 4979, 4919, 5209, 5417, 5659, 5577, 8117, 8119, 8739
+01_AE.CN.10.CYM136.JX112800, 256, 1752, 1713, 4556, 4501, 5079, 5019, 5309, 5525, 5770, 5688, 8243, 8245, 8871
+40_BF1.BR.04.04BRRJ115.EU735538, 330, 1835, 1805, 4648, 4593, 5171, 5111, 5401, 5613, 5858, 5776, 8364, 8366, 8998
+B.FR.08.DEMB08FR002.JX140654, 146, 1654, 1615, 4458, 4403, 4981, 4921, 5211, 5423, 5671, 5586, 8210, 8212, 8853
+BF1.ES.09.DEMBF09ES006.JX140661, 145, 1626, 1596, 4439, 4384, 4965, 4905, 5195, 5407, 5652, 5570, 8110, 8112, 8738
+B.BR.10.10BR_RJ078.KT427769, 271, 1764, 1725, 4568, 4513, 5091, 5031, 5321, 5533, 5778, 5696, 8257, 8259, 8897
+A6.UA.00.98UA0116.AF413987, 798, 2291, 2252, 5095, 5040, 5618, 5558, 5848, 6064, 6309, 6227, 8803, 1, 624
+01_AE.CN.05.FJ053.DQ859179, 806, 2305, 2266, 5109, 5054, 5632, 5572, 5862, 6078, 6323, 6241, 8823, 8824, 9444
+B.IN.x.11807.EF694037, 140, 1639, 1600, 4443, 4388, 4966, 4906, 5196, 5408, 5653, 5571, 8090, 8109, 8729
+B.US.x.L8146.DQ886034, 13, 1533, 1494, 4337, 4282, 4860, 4800, 5093, 5305, 5550, 5468, 8008, 8010, 8639
+B.US.14.2529.KX505475, 130, 1656, 1617, 4460, 4405, 4983, 4923, 5213, 5425, 5688, 5588, 8188, 8190, 8816
+84_A1D.SE.10.042SE.MF373153, 1, 1497, 1458, 4301, 4246, 4824, 4764, 5054, 5266, 5511, 5429, 7924, 7943, 8560
+01_AE.CN.07.FJ070017.JX112811, 257, 1744, 1705, 4548, 4493, 5071, 5011, 5301, 5517, 5762, 5680, 8277, 8279, 8899
+01B.TH.07.MERLBDTRC3.JN860762, 2, 1495, 1456, 4299, 4244, 4822, 4762, 5052, 5267, 5512, 5430, 7973, 7975, 8595
+A1BD.GB.16.DEURF16UK009.MN703144, 304, 1806, 1767, 4631, 4576, 5154, 5094, 5384, 5596, 5841, 5759, 8296, 8298, 8918
+B.US.06.502_0309_wg13.JF320048, 2, 1507, 1468, 4311, 4256, 4834, 4774, 5064, 5276, 5524, 5439, 8018, 8020, 8643
+A1D.UG.10.DEURF10UG016.KP109493, 94, 1593, 1554, 4397, 4342, 4920, 4860, 5150, 5372, 5617, 5535, 8147, 8149, 8778
+01_AE.CN.07.GD070120.JX112827, 243, 1745, 1706, 4549, 4494, 5072, 5012, 5302, 5518, 5763, 5681, 8260, 8262, 8882
+C.ZA.03.03ZASK232B1.DQ093589, 229, 1710, 1671, 4514, 4459, 4935, 4976, 5266, 5475, 5729, 5653, 8214, 8216, 8839
+C.ZA.03.03ZASK094B1.AY878070, 225, 1703, 1664, 4507, 4452, 5030, 4970, 5260, 5469, 5729, 5647, 8277, 8279, 8902
+B.US.08.HIV_US_BID_V4392_2008.JQ403087, 1, 1527, 1488, 4331, 4276, 4854, 4794, 5084, 5296, 5541, 5459, 8035, 8037, 8663
+B.US.12.T8250_FL_CON.KU901997, 289, 1797, 1758, 4601, 4546, 5124, 5064, 5354, 5566, 5811, 5729, 8284, 8286, 8903
+08_BC.CN.07.07CNYN344.KF835529, 157, 1632, 1593, 4436, 4381, 4962, 4902, 5192, 5401, 5649, 5567, 8149, 8151, 8786
+BC.CN.05.05YNRL20sg.KC898978, 1, 1476, 1437, 4280, 4225, 4806, 4746, 5036, 5246, 5500, 5418, 7958, 7960, 8580
+F1.x.03.LA21LeAn.KU168275, 817, 2310, 2280, 5123, 5068, 5646, 5586, 5876, 6098, 6343, 6261, 8786, 1, 624
+85_BC.CN.14.14CN_SCYB2.KU992929, 153, 1628, 1589, 4432, 4377, 4958, 4898, 5188, 5400, 5642, 5563, 8202, 8204, 8824
+57_BC.CN.07.341.HM776939, 157, 1644, 1605, 4448, 4393, 4974, 4914, 5204, 5413, 5661, 5579, 8107, 8109, 8735
+39_BF1.BR.03.03BRRJ327.EU735536, 184, 1686, 1647, 4490, 4435, 5013, 4953, 5243, 5455, 5700, 5618, 8155, 8157, 8798
+D.BR.10.10BR_RJ095.KJ787684, 244, 1746, 1707, 4550, 4495, 5073, 5013, 5303, 5515, 5760, 5678, 8230, 8232, 8864
+B.US.x.CR0036W.FJ469690, 15, 1508, 1478, 4321, 4266, 4844, 4784, 5074, 5286, 5531, 5449, 8019, 8029, 8646
+B.BR.05.05BR1079.JN692462, 230, 1729, 1690, 4533, 4478, 5056, 4996, 5286, 5498, 5743, 5661, 8231, 8233, 8880
+01_AE.CN.07.07CNYN327.KF835514, 176, 1669, 1630, 4473, 4418, 4996, 4936, 5226, 5442, 5702, 5620, 7554, 8143, 8748
+CF1.SE.13.086SE.MF373188, 1, 1479, 1440, 4283, 4228, 4806, 4746, 5234, 5254, 5505, 5423, 7960, 7962, 8579
+A6.RU.12.BLG035.MH330350, 150, 1646, 1607, 4450, 4395, 4973, 4913, 5203, 5419, 5664, 5582, 8167, 8169, 8792
+C.ZA.99.99ZALT4.EU293444, 791, 2266, 2227, 5070, 5015, 5593, 5533, 5823, 6032, 6292, 6210, 8741, 1, 621
+G.NG.11.DEMG11NG008.KY953202, 107, 1600, 1570, 4413, 4358, 4945, 4876, 5172, 5394, 5639, 5557, 8124, 8126, 8749
+B.US.95.5073_95.AY835768, 790, 2295, 2256, 5099, 5044, 5622, 5562, 5852, 6064, 6318, 6227, 8827, 8829, 9449
+46_BF1.BR.07.07BR_FPS812.HM026460, 240, 1727, 1688, 4531, 4476, 5054, 4994, 5284, 5506, 5751, 5669, 8239, 8241, 8843
+A1D.KE.05.05KE963379V4.KT022411, 2, 1504, 1465, 4308, 4253, 4831, 4771, 5061, 5273, 5518, 5436, 7997, 8000, 8611
+C.NP.07.11NP091.KU341730, 1, 1467, 1428, 4271, 4216, 4794, 4734, 5024, 5233, 5481, 5399, 7972, 7974, 8597
+01B.MY.05.05MYKL043_1.DQ366666, 175, 1674, 1635, 4478, 4423, 5001, 4941, 5231, 5447, 5692, 5610, 8189, 8191, 8811
+A1B.US.10.DEURF10US008.KC473836, 156, 1655, 1616, 4459, 4404, 4982, 4922, 5209, 5421, 5666, 5584, 8160, 8162, 8797
+B.CN.07.HB070035.JF932489, 243, 1745, 1706, 4549, 4494, 5072, 5012, 5302, 5514, 5759, 5677, 8211, 8213, 8848
+C.ZA.03.03ZAPS050MB1.DQ369980, 224, 1705, 1666, 4509, 4454, 5032, 4972, 5262, 5480, 5740, 5658, 8219, 8221, 8841
+B.KR.03.03HJY8.JQ316131, 473, 1975, 1936, 4779, 4724, 5302, 5242, 5532, 5744, 5989, 5907, 8501, 8503, 9123
+C.ZA.02.02ZAPS001MB1.DQ275648, 225, 1703, 1664, 4507, 4452, 5030, 4970, 5260, 5474, 5734, 5652, 8180, 8182, 8805
+01_AE.VN.97.97VNAG218.FJ185255, 54, 1550, 1511, 4354, 4299, 4877, 4817, 5107, 5323, 5568, 5486, 8029, 8031, 8651
+C.SE.14.097SO.MF373199, 1, 1488, 1449, 4292, 4237, 4815, 4755, 5045, 5264, 5524, 5442, 8015, 8017, 8643
+A6.RU.13.ARH047.MH330342, 104, 1585, 1546, 4389, 4334, 4912, 4852, 5142, 5358, 5603, 5521, 8082, 8084, 8713
+B.US.11.ES22_27.KF384808, 726, 2228, 2189, 5032, 4977, 5555, 5495, 5785, 5997, 6242, 6160, 8802, 8804, 9418
+01_AE.CN.07.GX070145.JX112836, 173, 1660, 1621, 4464, 4409, 4975, 4927, 5205, 5421, 5666, 5584, 8166, 8168, 8776
+C.SE.14.095CD.MF373197, 1, 1509, 1470, 4313, 4258, 4836, 4776, 5066, 5281, 5535, 5459, 8029, 8031, 8651
+02A1.PK.15.PK038.KX232627, 310, 1788, 1758, 4601, 4546, 5124, 5064, 5354, 5576, 5836, 5739, 8333, 8335, 8964
+A6.RU.13.ARH068.MH330346, 172, 1668, 1629, 4472, 4417, 4995, 4935, 5225, 5441, 5686, 5604, 8189, 8191, 8814
+A1C.SE.11.052SE.MF373155, 1, 1500, 1461, 4316, 4249, 4827, 4767, 5057, 5276, 5527, 5445, 7997, 8020, 8634
+A1C.IN.95.95IN21301.AF067156, 169, 1644, 1605, 4448, 4393, 4968, 4908, 5198, 5407, 5655, 5573, 8143, 8145, 8759
+BF1.BR.99.99BRRJSB067.MG365765, 723, 2216, 2186, 5029, 4974, 5552, 5492, 5782, 5994, 6239, 6157, 8664, 8666, 9283
+01_AE.CN.07.07CNYN329.KF835516, 175, 1671, 1632, 4475, 4420, 4998, 4938, 5228, 5444, 5689, 5607, 8180, 8182, 8802
+0209.CI.01.01IC_17395.AJ866554, 807, 2285, 2255, 5098, 5043, 5621, 5561, 5854, 6079, 6324, 6242, 8857, 1, 621
+B.DE.10.464704.KT124772, 1, 1503, 1464, 4319, 4252, 4830, 4770, 5060, 5272, 5517, 5435, 8035, 8037, 8666
+01_AE.CN.07.07CNYN332.KF835518, 173, 1672, 1633, 4476, 4421, 4999, 4939, 5229, 5445, 5690, 5608, 8163, 8165, 8767
+B.US.97.395718.KT124770, 1, 1506, 1467, 4310, 4255, 4833, 4773, 5063, 5275, 5520, 5438, 8059, 8061, 8690
+B.US.12.N8261_FL_CON.KU901976, 289, 1797, 1758, 4601, 4546, 5124, 5064, 5351, 5563, 5808, 5726, 8284, 8286, 8921
+C.ZA.03.03ZAPS099MB1.DQ275655, 224, 1702, 1663, 4518, 4451, 5029, 4969, 5259, 5468, 5728, 5646, 8225, 8227, 8856
+C.ZM.09.Z3678F_23Sep09_PL_NFLG_SGA19.KR820376, 211, 1710, 1671, 4526, 4459, 5037, 4977, 5267, 5486, 5734, 5652, 8192, 8194, 8889
+B.BR.03.03BR1020.JN692445, 247, 1764, 1725, 4568, 4513, 5091, 5031, 5324, 5537, 5791, 5709, 8309, 8311, 8958
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+C.ZA.03.03ZAPS125MB1.DQ396390, 226, 1701, 1662, 4517, 4450, 5028, 4968, 5258, 5467, 5727, 5645, 8227, 8229, 8849
+B.US.14.Pt2_DNA_28.KU678026, 87, 1598, 1559, 4402, 4347, 4925, 4865, 5149, 5361, 5609, 5524, 8136, 8139, 8756
+A1CD.KE.05.05KE215154V4.KT022400, 2, 1480, 1441, 4284, 4229, 4807, 4747, 5037, 5260, 5505, 5423, 8008, 8010, 8624
+01_AE.TH.10.40257v09_03.MN792331, 1, 1491, 1452, 4295, 4240, 4818, 4758, 5048, 5263, 5508, 5426, 8017, 8019, 8645
+DG.KE.06.06KECst_014.FJ623495, 2, 1489, 1459, 4302, 4247, 4825, 4765, 5055, 5277, 5522, 5440, 8019, 8021, 8650
+A1C.SE.11.060SE.MF373163, 1, 1503, 1464, 4307, 4252, 4830, 4770, 5060, 5279, 5530, 5448, 8081, 8083, 8706
+C.ZA.03.03ZASK026B2.DQ011165, 223, 1734, 1695, 4538, 4483, 5061, 5001, 5288, 5497, 5757, 5675, 8266, 8268, 8891
+B.US.97.1051_11.KT124744, 1, 1503, 1464, 4307, 4252, 4830, 4770, 5060, 5272, 5517, 5435, 8053, 8055, 8699
+BF1.BR.06.06BR_FPS561.HM026455, 243, 1739, 1700, 4543, 4488, 5066, 5006, 5296, 5518, 5763, 5681, 8233, 8235, 8870
+C.ZA.04.04ZASK174B1.AY901980, 226, 1722, 1683, 4526, 4471, 5049, 4989, 5279, 5488, 5748, 5666, 8287, 8289, 8912
+A6.RU.12.BLG038.MH330351, 115, 1611, 1572, 4415, 4360, 4938, 4878, 5168, 5384, 5629, 5547, 8123, 8125, 8736
+A1.KE.06.06KECst_019.FJ623478, 2, 1498, 1459, 4302, 4247, 4825, 4765, 5055, 5277, 5525, 5443, 8043, 8045, 8659
+C.ZA.03.03ZASK073B1.AY901970, 224, 1714, 1675, 4518, 4463, 5041, 4981, 5271, 5480, 5740, 5658, 8273, 8275, 8898
+D.UG.94.94UG114.U88824, 139, 1647, 1608, 4451, 4396, 4974, 4914, 5240, 5416, 5661, 5579, 8113, 8115, 8735
+C.BW.00.00BW17593.AF443094, 167, 1645, 1606, 4461, 4394, 4972, 4912, 5202, 5418, 5678, 5596, 8160, 8162, 8791
+01_AE.CN.07.JS071101.JX112853, 259, 1749, 1710, 4553, 4498, 5076, 5016, 5306, 5522, 5767, 5685, 8249, 8251, 8862
+B.SI.11.Sample29_SI257.MN736700, 295, 1791, 1752, 4595, 4540, 5118, 5058, 5345, 5557, 5802, 5720, 8248, 8250, 8885
+16_A2D.KE.05.05KE725124V4.KT022406, 2, 1489, 1450, 4293, 4238, 4816, 4756, 5043, 5265, 5510, 5428, 8004, 8006, 8626
+B.US.99.868558.KT124798, 1, 1518, 1479, 4322, 4267, 4845, 4785, 5075, 5287, 5532, 5450, 8029, 8031, 8651
+11_cpx.CM.11.DEURF11CM015.KP109503, 92, 1600, 1570, 4413, 4358, 4936, 4876, 5166, 5380, 5634, 5552, 8146, 8148, 8780
+02F2G.CM.02.LT66.JN864057, 88, 1563, 1533, 4376, 4321, 4911, 4842, 5132, 5354, 5599, 5517, 8111, 8113, 8730
+C.US.11.17TB4_4G8.KF526226, 120, 1643, 1604, 4447, 4392, 4970, 4910, 5200, 5419, 5679, 5597, 7540, 8164, 8817
+15_01B.TH.05.05TH522586.JN248351, 2, 1474, 1435, 4278, 4223, 4801, 4741, 5031, 5240, 5485, 5403, 7967, 7969, 8583
+C.BW.96.96BWM032.AF443075, 166, 1647, 1608, 4463, 4396, 4974, 4914, 5171, 5424, 5678, 5602, 8196, 8198, 8824
+A1.UG.09.DEMA109UG001.KF716478, 153, 1640, 1601, 4444, 4389, 4967, 4907, 5200, 5422, 5676, 5594, 8173, 8175, 8813
+C.ZM.02.02ZM108.AB254141, 789, 2261, 2222, 5077, 5010, 5588, 5528, 5818, 6036, 6296, 6214, 8853, 8855, 9481
+01_AE.CN.05.05GX162.GU564229, 27, 1514, 1475, 4318, 4263, 4841, 4781, 5071, 5287, 5532, 5450, 8005, 8007, 8627
+B.US.06.CR0222X.FJ469709, 23, 1525, 1486, 4329, 4274, 4861, 4792, 5082, 5294, 5539, 5457, 8060, 8062, 8676
+G.CM.05.05CMBDSH19.MN153484, 195, 1685, 1655, 4498, 4443, 5030, 4961, 5251, 5473, 5718, 5636, 8149, 8151, 8774
+55_01B.CN.10.HNCS102056.JX574661, 106, 1602, 1563, 4406, 4351, 4929, 4869, 5159, 5375, 5620, 5538, 8126, 8128, 8745
+A6.RU.12.BLG041.MH330352, 164, 1654, 1615, 4458, 4403, 4981, 4921, 5211, 5427, 5672, 5590, 8190, 8192, 8821
+02B.NG.15.20389v01.MH666162, 2, 1489, 1459, 4302, 4247, 4825, 4765, 5055, 5282, 5527, 5445, 7991, 7993, 8628
+C.ZA.03.03ZAPS094MB1.DQ396377, 225, 1700, 1661, 3601, 4448, 5026, 4966, 5256, 5465, 5728, 5646, 8222, 8224, 8859
+D.US.07.HIV_US_BID_V3121_2007.JQ403079, 1, 1503, 1464, 4307, 4252, 4830, 4770, 5060, 5272, 5517, 5435, 7999, 8001, 8636
+01_AE.CN.07.GX070143.JX112835, 173, 1663, 1624, 4467, 4412, 4990, 4930, 5220, 5436, 5681, 5599, 8190, 8192, 8809
+B.ES.08.P2008.FJ670531, 239, 1744, 1705, 4548, 4493, 5071, 5011, 5301, 5513, 5758, 5676, 8285, 8287, 8910
+B.TH.13.2544072P000FL_Sd.MG989506, 2, 1486, 1447, 4290, 4235, 4813, 4753, 5043, 5255, 5500, 5418, 7976, 7978, 8595
+A1.KE.04.04KE860822V3.KT022369, 2, 1498, 1459, 4302, 4247, 4831, 4771, 5061, 5283, 5528, 5446, 8028, 8030, 8644
+B.AR.14.DEMB14AR012.MH078531, 110, 1627, 1588, 4431, 4376, 4954, 4894, 5184, 5396, 5644, 5559, 8153, 8155, 8784
+B.US.13.CP02.KX505589, 79, 1605, 1566, 4409, 4354, 4932, 4872, 5162, 5374, 5631, 5546, 8149, 8151, 8786
+B.BR.05.05BR1077.JN692460, 126, 1631, 1592, 4435, 4380, 4958, 4898, 5188, 5400, 5645, 5563, 8184, 8186, 8800
+C.SE.05.010BI.MF373131, 1, 1500, 1461, 4304, 4249, 4827, 4767, 5057, 5273, 5536, 5454, 8045, 8047, 8703
+13_cpx.CM.96.96CM_1849.AF460972, 168, 1688, 1658, 4501, 4446, 5024, 4964, 5254, 5475, 5720, 5638, 8241, 8243, 8842
+01_AE.CN.10.DE00110CN007.KP109506, 164, 1660, 1621, 4464, 4409, 4987, 4927, 5217, 5433, 5678, 5596, 8205, 8207, 8812
+C.ZA.04.SK144B1.AY703911, 225, 1703, 1664, 4507, 4452, 5030, 4970, 5260, 5479, 5739, 5657, 8197, 8228, 8851
+B.JP.x.JRC05B.AB565497, 791, 2287, 2257, 5100, 5045, 5623, 5563, 5853, 6065, 6331, 6228, 8870, 8872, 9522
+C.NP.08.11NP084.KU341728, 1, 1482, 1443, 4286, 4231, 4809, 4749, 5039, 5248, 5496, 5414, 7987, 7989, 8612
+C.SE.09.031ER.MF373145, 1, 1494, 1455, 4298, 4243, 4821, 4761, 5051, 5270, 5530, 5448, 7997, 7999, 8622
+A1C.TZ.06.CO3651V7.KX907381, 2, 1483, 1444, 4287, 4232, 4810, 4750, 5040, 5259, 5519, 5437, 8031, 8033, 8656
+B.US.16.PID1683.PBMC_M18_03_WIPF1_F1F4_PBio.MN691961, 101, 1603, 1564, 4407, 4352, 4930, 4870, 5157, 5369, 5614, 5532, 8102, 8105, 8731
+BC.CN.05.05YNRL09sg.KC898977, 1, 1500, 1461, 4304, 4249, 4830, 4770, 5060, 5269, 5517, 5435, 8044, 8046, 8669
+C.SE.07.SE600119.KP411831, 1, 1467, 1428, 4271, 4216, 4794, 4734, 5024, 5246, 5587, 5424, 8033, 8035, 8658
+C.ZM.11.DEMC11ZM008.KP109496, 147, 1628, 1589, 4432, 4377, 4955, 4895, 5185, 5394, 5651, 5572, 8097, 8099, 8722
+B.US.x.F703.DQ886031, 16, 1542, 1503, 4346, 4291, 4869, 4809, 5099, 5311, 5556, 5474, 8032, 8034, 8675
+B.BR.16.2HU_UFRJ_2016.MK041551, 99, 1607, 1568, 4411, 4356, 4934, 4874, 5164, 5376, 5621, 5539, 8133, 8135, 8767
+B.CN.x.RL42.U71182, 162, 1679, 1640, 4483, 4428, 5006, 4946, 5236, 5448, 5693, 5611, 8148, 8150, 8770
+B.US.07.HIV_US_BID_V3044_2007.JQ403066, 1, 1518, 1479, 4322, 4267, 4845, 4785, 5075, 5293, 5553, 5456, 8041, 8043, 8663
+A6.RU.08.DEMA108RU003.KF716491, 151, 1641, 1602, 4445, 4390, 4968, 4908, 5198, 5414, 5659, 5577, 8156, 8158, 8781
+C.NP.09.11NP076.KU341726, 1, 1476, 1437, 4280, 4225, 4803, 4743, 5033, 5242, 5490, 5408, 8002, 8004, 8624
+BC.CN.07.309.HM776938, 158, 1636, 1597, 4440, 4385, 4966, 4906, 5196, 5408, 5653, 5571, 8126, 8128, 8751
+B.US.10.505_1962a.WG03.MG197136, 2, 1510, 1471, 4314, 4259, 4837, 4777, 5067, 5279, 5524, 5442, 8135, 8137, 8796
+B.US.99.284160.KT124759, 1, 1503, 1464, 4307, 4252, 4830, 4770, 5060, 5272, 5517, 5435, 8026, 8028, 8681
+B.DE.10.571373.KT124780, 1, 1509, 1470, 4313, 4258, 4836, 4776, 5066, 5278, 5523, 5441, 8014, 8016, 8612
+BC.BR.05.05_BR_NSP24.GQ365650, 374, 1897, 1858, 4701, 4646, 5224, 5164, 5454, 5666, 5917, 5835, 8417, 8419, 9042
+B.CN.07.FJ070016.JF932483, 37, 1539, 1500, 4343, 4288, 4866, 4806, 5096, 5308, 5553, 5471, 8029, 8031, 8648
+B.JP.08.NMC104_clone_01.AB731663, 796, 2307, 2277, 5126, 5071, 5649, 5589, 5879, 6091, 6366, 6254, 8824, 8826, 9464
+A1.KE.06.06KECst_028.FJ623479, 2, 1498, 1459, 4302, 4247, 4825, 4765, 5055, 5277, 5525, 5443, 8022, 8024, 8638
+H.CD.01.CG_0538_02_NGSID15.KY392778, 811, 2307, 2268, 5111, 5056, 5637, 5577, 5867, 6076, 6318, 6236, 8794, 8797, 9420
+D.ZA.84.R2.AY773338, 52, 1557, 1518, 4364, 4309, 4887, 4827, 5117, 5329, 5574, 5492, 8032, 8034, 8657
+0108.CN.12.GXDY_1299_NLFG.KF541292, 154, 1677, 1638, 4481, 4426, 5007, 4947, 5237, 5453, 5701, 5616, 8240, 8242, 8853
+01_AE.CN.07.FJ070035.JX112814, 94, 1593, 1554, 4397, 4342, 4920, 4860, 5150, 5366, 5611, 5529, 8108, 8110, 8739
diff --git a/bin/CodonCorrectionReferences/HIV1_ALL_2020_genome_DNA_no_ambiguity_only_annotated_aligned_no_gap_columns_aligned.fasta b/bin/CodonCorrectionReferences/HIV1_ALL_2020_genome_DNA_no_ambiguity_only_annotated_aligned_no_gap_columns_aligned.fasta
new file mode 100644
index 0000000..3de5043
--- /dev/null
+++ b/bin/CodonCorrectionReferences/HIV1_ALL_2020_genome_DNA_no_ambiguity_only_annotated_aligned_no_gap_columns_aligned.fasta
@@ -0,0 +1,3584 @@
+>B.FR.83.HXB2_LAI_IIIB_BRU.K03455
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+>A.CD.87.P4039.MH705157
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+>A.CH.03.HIV_CH_BID_V3538_2003.JQ403028
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+>A1.BG.09.V_09_017.MH746253
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+>A1.CD.87.70641.MH705151
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+>A1.CD.87.PBS6126.MH705153
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+>A1.CD.87.PBS888.MH705133
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+>A1.CM.07.46_10.KP718918
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+>A1.CM.08.886_24.KP718928
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+>A1.IN.99.NARI_FLS_VB81_12.KT152844
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+>A1.KE.04.04KE263806V2.KT022361
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+>A1.KE.06.06KE196199V6.KT022378
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+>A1.KE.06.06KE335214V6.KT022380
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+>A1.KE.06.06KE404877V7.KT022381
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+>A1.KE.06.06KE452693V6.KT022382
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+>A1.KE.06.06KECst_006.FJ623475
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+>A1.KE.06.06KECst_019.FJ623478
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+>A1.KE.06.06KECst_021.FJ623477
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+>A1.KE.97.ML013_2.AY322185
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+>A1.KE.97.ML605_3.AY322190
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+>A1.KE.97.ML752.AY322193
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+>A1.PK.14.PK001.KX232594
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+>A1.PK.15.PK021.KX232614
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+>A1.PK.15.PK034.KX232624
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+>A1.PK.15.PK036.KX232626
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+>A1.RW.11.DEMA111RW002.KF716472
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+>A1.RW.92.92RW008.AB253421
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+>A1.SE.12.064GR.MF373167
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+>A1.SE.12.065SE.MF373168
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+>A1.TZ.04.CO0272V4.KX907336
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+>A1.TZ.05.CO0439V5.KX907347
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+>A1.TZ.06.CO6637V7.KX907414
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+>A1.TZ.06.CO6830V7.KX907423
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+>A1.TZ.06.CO6974V7.KX907431
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+>A1.UG.09.DEMA109UG001.KF716478
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+>A1.UG.11.10203v01_01.MN791169
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+>A1.UG.11.DEMA110UG001.KF859745
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+>A1.UG.11.DEMA110UG009.KF716486
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+>A1.UG.92.UG029.AB098333
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+>A1.UG.x.UG031.AB098331
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+>A1.UG.x.UG275.AB485632
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+>A1.ZA.04.503_15344_T10_A1.KT183312
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+>A2.CD.87.PBS1195.MH705163
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+>A6.RU.12.BLG015.MH330347
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+>A6.RU.12.BLG032.MH330348
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+>A6.RU.12.BLG033.MH330349
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+>A6.RU.12.BLG035.MH330350
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+>A6.RU.12.BLG038.MH330351
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+>A6.RU.12.BLG041.MH330352
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+>A6.RU.12.BLG043.MH330353
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+>A6.RU.12.BLG044.MH330354
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+>A6.RU.12.BLG045.MH330355
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+>A6.RU.12.BLG051.MH330356
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+>A6.RU.13.ARH001.MG902950
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+>A6.RU.13.ARH011.MG902951
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+>A6.RU.13.ARH028.MH330337
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+>A6.RU.13.ARH033.MH330339
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+>A6.RU.13.ARH036.MH330340
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+>A6.RU.13.ARH042.MH330341
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+>A6.RU.13.ARH047.MH330342
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+>A6.RU.13.ARH061.MH330344
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+>A6.RU.13.ARH066.MH330345
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+>A6.RU.13.ARH068.MH330346
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+>A6.RU.14.DEMA614RU024.MT222948
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+>A6.SI.09.Sample25_SI209.MN736699
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+>A6.UA.00.98UA0116.AF413987
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+>A7.NG.11.DEURF11NG005.MH078558
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+>B.AR.07.DEURF07AR001.KY658686
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+>B.AR.09.DEMB09AR010.MH078530
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+>B.AR.10.DEMB10AR006.KY658684
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+>B.AR.14.DEMB14AR012.MH078531
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+>B.AR.15.DEMB15AR013.MH078532
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+>B.AU.86.MBC200.AF042100
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+>B.AU.87.MBC925.AF042101
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+>B.AU.95.C76.AF538306
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+>B.AU.99.1181.AF538302
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+>B.AU.x.VH_VHPCR.AF146728
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+>B.BE.17.02006_cen.MN449474
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+>B.BG.08.P_08_001.MH746266
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+>B.BG.08.P_08_004.MH746265
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+>B.BG.08.S_08_001.MH746264
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+>B.BG.08.V_08_001.MH746261
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+>B.BR.02.02BR002.DQ358805
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+>B.BR.02.02BR008.DQ358808
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------agtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ctgaaagtgaaag------------------------------------------tagaaccagagga--------gctctctcgacgca-ggactcggcttgct---gaagcgcgcacagcaagaggc-------------gagg-gg--cggc-----gactggtgagtacgcc--------------------------attttttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggagaattagataaatgggagaaaattcggtta---agg------cca---gggggaaagaaacaatataaattaaaacatatagtatgggcaagcagggaactagaacgcttcgcagttaaccctggccttttagagacagcagaaggctgtagacaaatactagcacagctacagccatcc---cttcagacaggatcagaagaacttagatcattatataatacagta---gcaaccctctattgtgtgcatcaaaagatagatgtaaaagacaccaaggaggctttagacaagatagaggaagagcaaaacaaatgtaag------------------------caaaaggcacagcaagcagcagct---------------------gacgcagga------------------aac---agcaaaccg------------------------gtcagccaaaattaccctata------------gtgcagaacatccaggggcaaatggtacatcaggccctatcacctagaactttaaatgcatgggtaaaagtaatagaagacaag------gctttcagcccagaagtaatacccatgttctcagcattatcagaaggagccaccccacaggatttaaacactatgctaaacacagtggggggacatcaa---gcagccatgcaaata---ttaaaagag---accatcaatgaggaagctgcagattgggatagattgcat---ccagtgcatgca---gggcctgctgcgccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaataggatggatgaca---------agcaatcca---cct---atc---ccagta---ggagaaatctataagagatggataatcctgggattaaataaaatagtaagaatgtatagccctgttagtattctggacataagacaaggaccaaaggaaccctttagagattatgtagaccggttctataaaactctaagagccgagcaagcttcacaggatgtaaaaaattggatgacagaaaccttgttggtccagaatgcgaacccagattgtaaaactatcttaaaagcattgggaccagcagctacactagaagagatgatgacagcatgccagggagtgggaggacccggccacaaa---gcaagagttttggctgaa------gcaatg---agccaagtaaat------------------------acaaataccata---atgatg------cagagaggcaat---------ttt---aggaatcaaagaaag------actgttaagtgtttcaattgtggcaaagaaggg---catatagccagaaattgcagggcccctaggaaaaagggctgttggaaatgtggaagggaaggacaccaaatgaaagattgc---------------actgagagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---aag---gccaggaaactttcctcagagcagaacagagccaacagc------------------------------------------------------cccaccaga------agagagcttcaggtt------------tggggaggagacaacaac---tccccc------------------------------tcagaa---------------gcaggagcc------------gatggacaa---------------------------gga------------actata------tcctttagcttccctcaaatcactctttggcagcgacccatcgtctcaataaagataggggggcaattaaaggaagctctattagatacaggagcagatgatacagtatta---gaagaa---atgaatttgccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcagatacttgtagaaatttgtggacataaagcaataggtacagtattagtaggacctacacctgtcaac---ataattggaagaaatctgttgactcagcttggctgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattgaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaagcattagtagaaatttgtaca------gaaatggaaaaggaaggaaaaatttcaaaa---attgggcct---gaaaatccatacaatactccagtatttgccataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctgggaa---gttcaa------tta---ggaata---------------------------ccacatcccgcagggttgaaaaagaaa---aaa------tcagtaacagtactggatgtgggtgatgcatat---ttttcagttcctttacatgaagacttcagaaagtatactgcatttaccatacctagtacaaacaatgagacaccagggattagatatcagtacaatgtgctgccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaattttagaaccttttaggaagcaaaatccagacgtagttatctaccaatacatggatgatttgtatgtaggatctgacttagaaatagggcagcatagaacaaaaatagaggaactgagacaacatctgttgaagtgggggtttaccacaccagacaaaaaacatcagaaagaacccccatttctttggatgggttatgaactccatcctgataaatggacagtacaacctatagtactgccagac---aaagac---agctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttatgcagggattaaagtaaggcaattatgtaaactcattaggggaaccaaagcactaacagaagtagtaacattaacaaaagaagcagagctagaactagcagaaaacagggagattctaaaagaaccagtacatggggtgtattatgacccatcaaaagacttaatagcagaaatacagaagcaggggcaaggtcaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaagtatgcaagaatg---aggggggcccacactaatgatgta------aaacaattaacagaggcagtgcaaaaagtagccacagaaagcatagtaatatggggaaag---attcctaaatttaagttacccatacaaaaagaaacatgggaagcatggtggacagagtattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagtgaaactatggtatcagttagagaaagaacccataatgggagcagaaactttctatgtagatggggcagctaatagggaaactaaattaggaaaagcaggatatgtaactgacagaggaagacaaaaa---gttgtccccctacaggacacaacaaatcagaagtctgagttacaagcaattcatctagctttgcaggattcaggattagaag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+>B.BR.02.02BR011.DQ358809
+------------------------------------------------------------------------------------------------------ccaggg-atcagatatccactgacctttggatggtgcttcaagctagtaccagttgacccacagcaagtagaagag--gcc---actcaaggagagaccaactgcttg-tacaccccttgaaccagcatgggatggatgacccagagaaagaagtgttacagtggaagtttgacagcaaactagcattc---catcacgtggcccgagagaaa------cat--ccggagtac------------------------tacaaagactgctga-----------------------------------cagcgagtttt------------ctac---aa--gggactttcc-------------------gct--ggggactttcca-ggga-ggtgtggct--------------tgggg-cggtact-gggg-agtggc-gag-ccctcaga-tgctgcatataagcag-ctgctttttgcctgtact-g-ggtctctc--tggttagaccagatc-t-gagcctgggagctctctgg-ctaac-taagg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-ttc--aa-g-----ta-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccatt-taag-t-cagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct--gaaagcgcgctcggcaagaggc-------------gagg-gg--cggc-----gactggtgagtacgcc-------------------aaacataaaattttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggaaaattagataaatgggaaaaaattcggtta---agg------cca---gggggaaagaaacactataaattaaaacatatagtatgggcaagcagggagttagaacgattcgcacttaatcctggccttttagaaacaggagaaggctgtagacaaatattgggacagctacagtcatcc---cttcagacaggatcagaagaacttaaatcattatttaatgcagta---gcagtcctctattgtgtgcatcaaaatatagaggtaaaagataccaaggaagctttagacaagatagaggaagagcaaaacaaaagtaga------------------------aaaaaggcacagccagccgaagct---------------------gacacagga------------------aac---agcagcaag------------------------gtcagccaaaattatcctata------------gtgcagaacctccaggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgggtaaaagtaatagaagagaag------gctttcagcccggaggtaatacccatgttttcagcattatcagaaggagccaccccacaagatttaaacaccatgctaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagag---accatcaatgaggaagctgcagaatgggatagattgcat---ccagcgcaggca---gggcctgttgcgccaggccagatg---agagacccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaataggatggatgaca---------agtaatcca---cct---atc---ccagta---ggagaaatttataaaagatggataatcctgggattaaataaaatagtaagaatgtatagccctgtcagcattctggacataagacaaggaccaaaggaaccctttagggactatgtagacaggttctataaaactctaagagccgagcaagcttcacaagatgtaaaaaattggatgacagaaaccttgttggtccagaatgcgaacccagattgtaagactattttaaaagcattgggaccagcagctacactagaagaaatgatgacagcatgtcagggagtggggggacccggccataaa---gcaagagttttggctgaa------gcaatg---agtcaagtaaca------------------------cacacaaacgta---atgatg------cagaaaggcaac---------ttt---aggaaccaaagaaga------attgttaagtgtttcaattgtggcaaagaaggg---catatagccaaaaattgcagggcccctagaaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagattgt---------------actgagagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---gag---gccaggaaatttctttcagagcagaccagagccaacagc------------------------------------------------------cccaccaga------agagagcttcaggtt------------tggggaagagacaacaac---tctctc------------------------------tcagaa---------------gcaggagac------------gggagacaa---------------------------gga------------actgta---tcctcctttagcttccctcaaatcactctttggcaacgaccagtagtcacaataaaagtaggggggcaactaaaggaagccctattagatacaggggcagataatacagtatta---gaagaa---atgaatttgccaggaaaatggaaaccaagaatgatagggggaattggaggttttatcaaagtaaaacagtat---gatcagatacccttagaaatctgtgggcatagagctataggtacagtgttaataggacctacgcctgtcaat---ataattggaagagatctcttgactcagattggctgcactttgaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaagcattagtagaaatttgtaca------gaaatggaaaaggaaggaaaaatttcaaga---attgggcct---gaaaatccatacaatactccaatatttgccataaagaaaaagaacagt------actagatggagaaaattagtagatttcagagaacttaataaaagaactcaagatttctgggag---gttcaa------tta---ggaata---------------------------ccacatcccgcagggttaaaaaagaaa---aaa------tcagtaacagtactggatgtgggtgatgcatat---ttttcagttcccttagataaagaattcaggaagtatactgcatttaccatacctagtacaaacaatgagacaccggggattaggtatcagtacaatgtgctcccacagggatggaaaggatcaccagcaatatttcaaagcagcatgacaaaaatcttagaaccttttagaaaacaaaatccagaaatagttatctatcaatacgtggatgatttgtatgtaggatcggacttagaaataggacagcatagagcaaaaatagaggaactgagacaacatctgttgaggtggggattaaccacaccagaccaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataagtggacagtacagcctataacgctgccagaa---aaagat---agctggactgtcaatgacatacagaagttagtaggaaaattaaattgggcaagccagatttatccagggattaaagtaaagcaattatgtaaactccttaggggaaccaaagcactaacagaagtagtaccactaacagaagaagcagagctagaactggcagaaaacagggagattctaaaagaaccagtacatggggtgtattatgacccatcaaaagacttaatagcagaaatacagaagcaggggcagggccaatggacatatcaaatttatcaagaaccatttaagaatctgaaaacaggaaagtatgcaagaatg---aggggtgcccacactaatgatgta------aaacaattaacagaagcagtgcaaaaaatagccacagaaagcatagtaatatggggaaag---attcctaaatttaaattacccatacaaaaagagacatgggaaacatggtggatagagtattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagtaaaattatggtaccagttagagaaagaacccatagtaggagcagaaaccttctatgtagatggggcagctaatagagaaactaaattaggaaaagcaggatatgttactgacagaggaagacaaaag---gctgtctccctaacggacacaacaaatcagaagactgagttacaagcaattcatctagctttgcaggattcgggatcagaag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+>B.BR.02.02BR013.DQ358810
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+>B.BR.02.02BR1013.JN692432
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+>B.BR.02.02BR2025.JN692435
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+>B.BR.02.02BR2032.JN692439
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+>B.BR.02.02BR2033.JN692440
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+>B.BR.02.02BR2041.JN692443
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+>B.BR.02.02BR2042.JN692444
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+>B.BR.02.04BR1064.JN692433
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+>B.BR.03.03BR1020.JN692445
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+>B.BR.03.BREPM1023.EF637057
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+>B.BR.03.BREPM1024.EF637056
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+>B.BR.03.BREPM1027.EF637054
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+>B.BR.03.BREPM1028.EF637053
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+>B.BR.03.BREPM1032.EF637051
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+>B.BR.03.BREPM1033.EF637050
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+>B.BR.03.BREPM1035.EF637049
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+>B.BR.03.BREPM1038.EF637048
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+>B.BR.03.BREPM1040.EF637047
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+>B.BR.03.BREPM2012.EF637046
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+>B.BR.04.04BR1047.JN692450
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+>B.BR.04.04BR1049.JN692451
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gc-ttc--aa-g-----ta-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccctt-ttag-t-cagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------gcgaaagcgaaag------------------------------------------taaagccagagga--------gaactctcgacgca-ggactcggcttgct---gaagcgcgcacggcaagaggc-------------gagg-gg--cggc-----gactggtgagtacgcc------------------------aaaaattttgact----------agcaga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggacaattagacaaatgggagaaaattcggtta---cgg------cca---gggggaaagaaacaatataaattaaaacatatagtatgggcaagcagggagctagaacgattcgcagtcaaccctggccttttagagtcagcagaaggctgtagacaaatattggaacagctacaaccagcc---cttaagacaggatcagaagaacttagatcattatataatacagta---gcaaccctctattgtgtacatcagaagatagaggtaaaagataccaaggaagctttagacaaaatagaggaagagcaaaacaaaggtaat------------------------aaaaaagcacagcaagtagcaact---------------------aacacagga------------------aac---atcaaccag------------------------gttagtcaaaattaccctata------------gtgcaaaaccttcaggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgggtaaaagtagtagaagagaag------gcctttagcccagaagtgatacccatgttttcagcattatcagaaggagccaccccacaagatttaaacaccatgctaaacacagtggggggacaccaa---gcagctatgcaaatg---ttaaaggag---accatcaatgaggaagctgcagagtgggatagaatacat---ccagtgcatgca---ggacctgttgcaccaggtcagatg---agagaaccaaggggaagtgacatagcaggaactaccagtacc---ctgcaggaacaagtaggatggatgaca---------agtaatcca---cct---atc---ccagta---ggagaaatttataagagatggataatactaggattaaataaaatagtaagaatgtatagccctaccagcattctggacataagacaaggaccaaaggaaccctttagagactatgtagaccggttctataaaactctaagagccgagcaagcttcacaggaggtaaaaaattggatgacagaaaccttgttggtccaaaatgcgaacccagattgtaagactattttaaaagcattaggaccagcagctaccctagaagaaatgatgacagcatgtcagggagtgggagggcccggacataaa---gcaagggttttggctgaa------gcaatg---agccaagtgacaggt---------------------caagctaacata---atgatg------cagagaggcaat---------ttt---aggaaccaaagaaag------actattaagtgtttcaattgtggcaaagagggg---cacatagccaaaaattgcagggcccctagaaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagattgt------------tctcttgaaagacaggctaattttttagggaaaatctggcc---ttcccagaa------ggg---aag---gccgggaaatttccttcagagcagaccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------tggggaagagacaacaac---tccccc------------------------------tcagaa---------------acaggagcc------------gatagacaa---------------------------gga------------actgta------tcccttagcttccctcaaatcactctttggcaacgacccctcgtcccaataagggtagaggggcaactaaaggaagctctattagatacaggagcagatgatacagtatta---gaagac---atgagtttgccaggaaaatggaaaccaaaaatgatagggggaattggaggttttatcaaggttagacagtat---gatcagatagctatagaaatttgtggacataaagctataggtacagtactagtaggacctacacctgtcaac---ataattggaagaaatctgttgactcagattggttgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccgttgacagaagaa---aaaataaaagcattagtagaaatttgtaca------gaaatggaaaaggaaggaaaaatttcaaaa---attgggcct---gaaaatccatacaatactccagtatttgccataaggaaaaaagacagt------actaaatggagaaaattagtagatttcagagaactcaataagagaactcaagacttctgggaa---gttcaa------tta---ggaata---------------------------ccacaccccgcagggttaaaaaagaaa---aaa------tcagtaacagtactggatgtgggtgatgcatat---ttttcagttctattacatgaagacttcaggaagtatactgcatttaccatacctagtacaaacaatgagacaccaggaattagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaaaatcttagagccttttagaaaacaaaatccagaaatggttatctatcaatacatggatgatttgtatgtaggatctgacctagaaatagggcaacatagaacaaaaatagaggaactgagacaacatctattgaagtggggatttaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctataatgctgccagaa---aaagac---agctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttatccagggattaaagtaaggcaattatgtaaactcattaggggaaccaaagcattaacagaagtagtaccactaacagcagaagcagaactagaactggcagaaaacagggagattctaaaagaaccagtacatggggtatattatgacccaacaaaagacttgatagcagaaatacagaagcaagggcaaggccaatggacatatcagatttatcaagaaccatttaaaaatctaaaaacaggaaagtatgcaagaatg---aggggtgcccacactaatgatgtt------aaacaattaacagaggcagtgcaaaaaataaccacagaaggcatagtaatatggggcaag---attcctaaatttagattacccatacaaaaggaaacatgggaaacatggtggacagagtattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagtgaaattatggtaccagttagagaaggaacccataataggagcagaaactttctatgtagatggggcagctaatagagaaactagactaggaaaagcaggatatgttactgacaaaggaagacaaaag---gttgtctccataacagacaccactaatcagaagactgaattacaagcagttcatctagctttacaggattcgggattagaag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+>B.BR.04.04BR1051.JN692452
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+>B.BR.04.04BR1054.JN692453
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+>B.BR.04.04BR1055.JN692454
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+>B.BR.04.04BR1057.JN692455
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+>B.BR.04.04BR1068.JN692457
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+>B.BR.04.BREPM1066.FJ195090
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+>B.BR.04.BREPM1070.FJ195086
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+>B.BR.05.05BR1077.JN692460
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+>B.BR.05.05BR1078.JN692461
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+>B.BR.05.05BR1079.JN692462
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+>B.BR.05.05BR1080.JN692463
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+>B.BR.05.05BR1082.JN692465
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+>B.BR.05.05BR1089.JN692467
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+>B.BR.05.05BR1092.JN692468
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+>B.BR.05.05BR1095.JN692471
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+>B.BR.05.05BR1101.JN692473
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+>B.BR.05.05BR1104.JN692474
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+>B.BR.05.05BR1107.JN692475
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+>B.BR.05.BREPM1081.FJ195091
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+>B.BR.05.BREPM1084.FJ195088
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+>B.BR.05.BREPM1093.FJ195089
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+>B.BR.06.06BR1115.JN692479
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+>B.BR.06.06BR1119.JN692480
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+>B.BR.09.DEMB09BR040.KU749389
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+>B.BR.10.10BR_MG020.KT427682
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+>B.BR.10.10BR_MG039.KT427675
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+>B.BR.10.10BR_PE030.KT427733
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+>B.BR.10.10BR_PE049.KT427717
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+>B.BR.10.10BR_PE061.KT427870
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+>B.BR.10.10BR_PE095.KT427700
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+>B.BR.10.10BR_RJ019.KT427786
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+>B.BR.10.10BR_RJ040.KT427650
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+>B.BR.10.10BR_RJ050.KJ849811
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+>B.BR.10.10BR_RJ054.KJ849814
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+>B.BR.10.10BR_RJ078.KT427769
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+>B.BR.10.10BR_RJ086.KT427764
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+>B.BR.10.10BR_RJ097.KT427757
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+>B.BR.10.10BR_SP002.KT427830
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+>B.BR.10.10BR_SP007.KT427826
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+>B.BR.10.10BR_SP045.KJ849808
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+>B.BR.10.10BR_SP051.KT427803
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+>B.BR.10.DEMB10BR038.KU749390
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+>B.BR.16.19HI_2016.MK041586
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+>B.BR.16.2HU_UFRJ_2016.MK041551
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+>B.BR.16.HI2016_12.MG571987
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+>B.CA.06.502_1799_FL02.JF320427
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+>B.CA.96.WC10C_4.AY314056
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+>B.CA.97.CANB3FULL.AY779553
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+>B.CH.00.HIV_CH_BID_V3529_2000.JQ403022
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+>B.CH.01.HIV_CH_BID_V3531_2001.JQ403024
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+>B.CH.01.HIV_CH_BID_V3533_2001.JQ403025
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+>B.CH.01.HIV_CH_BID_V3534_2001.JQ403026
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+>B.CH.02.HIV_CH_BID_V3511_2002.JQ403019
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+>B.CH.02.HIV_CH_BID_V3539_2002.JQ403029
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+>B.CH.03.HIV_CH_BID_V4470_2003.JQ403045
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+>B.CH.04.HIV_CH_BID_V4408_2004.JQ403042
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+>B.CH.08.M2_0803101_NFLG8.KC797225
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+>B.CH.x.HK_JIDLNBL_S129.MT155020
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+>B.CN.02.02HNsc11.DQ007903
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+>B.CN.03.SHXDC0081.JF932492
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+>B.CN.05.05CNHB_hp3.DQ990880
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+>B.CN.07.AH070014.JF932469
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+>B.CN.07.AH070017.JF932470
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------act---ctggt-a---------------actagagatc-------cctcagacactt-ttag-t-cagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------tgagaccagagga--------gctctctcgacgca-ggactcggcttgct---gaagcgcgcacagcaagaggc-------------ga-g-ag--cggc-----gactggtaagtacgcc--------------------------attttttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggacaattagatagatgggaaaaaattcggtta---agg------cca---gggggaaagaaaacatataaattaaaacatatagtatgggcaagcagggagctagaacgattcgcaattaatcctggcctgttagaaacatcagaagggtgtagacaaatactgcaacaactacaaccagcc---cttccgacaggatcagaagaatgtaggtcattattcaatgcagta---gcagtcctctattgtgtacatcaaaggatagatataaaagacaccaaggaagctttagataagatagaggaagagcaaaacaaaagtaag------------------------aaaaaggcacagcaaacagcagct---------------------gacttagga------------------aat---aacagccag------------------------gtcagccaaaattaccctata------------gtgcaaaacctccaggggcaaatggtacatcagcccatatcacctagaactttaaatgcatgggtaaaagtagtagaagagaag------gcttttagtccagaagtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgctaaacacagtggggggacatcaa---gcagctatgcaaatg---ttaaaagaa---actatcaatgaggaagctgcagaatgggatagactgcat---ccagtgcaggca---gggccaattgcaccaggccagata---agagaaccaaggggaagtgacatagcaggaactactagcacc---cttcaggagcaaatagcatggatgaca---------cataatcca---cct---gtc---ccagta---ggagaaatctataaaagatggataatcctggggttaaataaaatagtaagaatgtatagccctaccagcattctggacataagacaaggaccaaaggaaccctttagagactatgtagaccggttctataaaactctaagagccgagcaagcttcacaagatgtaaaaaattggatgacagaaaccttgttggtccaaaatgcgaacccagattgtaggactattttaaaagcattaggaccagcagctacactagaagaaatgatgacagcatgtcagggagtggggggacccagccataaa---gcaaaaattttggctgaa------gcaatg---agccaagtaacaaattca---------------gcagcagctagtata---atgatg------cagagaggcaac---------ttt---aggaaccaaagaaag------attgtcaagtgtttcaattgtggcaaagaaggg---cacatagccaaaaattgcagggcccctagaaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaggattgt---------------actgaaagacaggctaattttttagggaagatctggcc---ttcccacaa------ggg---gag---gccagggaacttccttcagagcaggccagagccaacagc------------------------------------------------------cccaccaga------ggagagcttcaggtt------------tggggaagagacaacaac---tccccc------------------------------tcagaa---------------gcaggagcc------------aatagacaa---------------------------gga------------actata------tcctttaacctccctcaaatcactctttggcaacgacccctcgtcacaataaagataggggggcaattaaaggaagctctattagatacaggagcggatgatacagtatta---gaagaa---atgaatttgccagggagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcagatacccatagaaatctgtggacacaaaactgaaggtacagtattaataggacctacacctgtcaac---ataattgggagaaatctgttgactcagcttggttgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaagcattagtagaaatttgtaca------gaaatggaaaaggaagggaaaatttcaaaa---atcgggcct---gaaaatccatacaatactccagtatttgccataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagggaacttaataaaagaactcaagacttctgggaa---gttcaa------tta---ggaata---------------------------ccacatcctgcaggtttaaaaaagaaa---aaa------tctgtaacagttctggatgtgggtgatgcatat---ttctcagtccctttagataaagacttcaggaagtatactgcatttaccatacctagtgtgaacaatgagacaccagggatcagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaatgtagtatgacaaaaatcttagaaccttttagaaaacagaatccagacatagttatctatcaatacatggatgatttgtatgtaggatctgacttagaaatagggcagcatagaacaaaaatagaggaactgagacaacatctgttgaggtggggatttaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagagctgccagaa---aaggac---agctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttatgcagggattaaggtaagggagttatgtaaactccttaggggaaccaaagcactaacagaagtaataccactaacagaagaagcagagctagaactggcagaaaacagggaaattctgaaagagccagtacatggagtgtattatgacccatcaaaagacttaatagcagaaatacagaagcaggggctaggccaatggacataccaaatctatcaagagccatttaaaaatctgaaaacaggaaaatatgcaagaatg---aggggtgcccacactaatgatgta------aaacaattaaccgaggcagtacaaaaaatagcaatggaatgcatagtaatatgggggaag---actcctaaatttaaactacccatacaaaaggaaacatgggaagcatggtggacagagtattggcaagccacctggattcctgagtgggagtttaccaatacccctcccttagtaaaattatggtatcagttagaaaaagaacccatagaaggagcagaaactttctatgtagatggggcagctagtagggagactaaattaggaaaagccggatatgttactaacaaaggaagacaaaaa---gttgtcactctaactgacacaacaaatcagaagactgagttacaagcaattcatttagctttgcaggattcaggagcagaag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+>B.CN.07.AH070018.JF932471
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+>B.CN.07.AH070057.JF932472
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+>B.CN.07.BJ070030.JF932473
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+>B.CN.07.CBJC261.JF932474
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+>B.CN.07.CBJC392.JF932475
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+>B.CN.07.CBJC394.JF932476
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+>B.CN.07.CBJC396.JF932477
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+>B.CN.07.FJ070016.JF932483
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+>B.CN.07.GS070017.JF932484
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+>B.CN.07.GZ070002.JF932485
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+>B.CN.07.GZ070030.JF932486
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+>B.CN.07.HB070006.JF932487
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+>B.CN.07.HB070022.JF932488
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+>B.CN.07.HB070035.JF932489
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+>B.CN.07.JL070038.JF932490
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+>B.CN.07.JS070389.JF932491
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+>B.CN.07.SX070080.JF932493
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+>B.CN.07.hb070025.JF932499
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+>B.CN.07.hen1345.JF932500
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+>B.CN.08.CBJC489.JF932479
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+>B.CN.08.CBJC500.JF932480
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+>B.CN.08.CBJC503.JF932481
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+>B.CN.08.cbjc468.JF932498
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+>B.CN.09.09YNRL215042sg.KC899011
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+>B.CN.09.YN09P0014.JF932494
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+>B.CN.09.ZK042.JF932497
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+>B.CN.10.DEMB10CN002.JX140658
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+>B.CN.12.DEMB12CN006.KP109511
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+>B.CN.12.DEMB12CN010.KP109512
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+>B.CN.98.YN9802.JF932495
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+>B.CN.98.YN9838.JF932496
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+>B.CN.99.plwj.GU177863
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+>B.CN.x.RL42.U71182
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+>B.DE.04.9213_d0.JQ416158
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+>B.DE.04.963987.KT124812
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+>B.DE.04.HIV_DE_BID_V4131_2004.JQ403037
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+>B.DE.08.154162.KT124752
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+>B.DE.08.654207.KT124789
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+>B.DE.16.9253_W0_4F3_S90.MK115918
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+>B.DE.16.9254_wk_2_6_E19.MW063064
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+>B.DE.17.Strain0526.MK086129
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+>B.DE.86.D31.U43096
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+>B.DE.86.HAN.U43141
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+>B.DE.x.DEMBXXDE001.KC596067
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+>B.DK.01.CTL_016.EF514704
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+>B.DK.07.PMVL_011.FJ694790
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+>B.DO.11.DEMB11DR001.KY658702
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+>B.ES.06.R14.KT200350
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+>B.ES.08.P2008.FJ670531
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+>B.ES.08.R11.KT200349
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+>B.ES.08.R5.KT200354
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+>B.ES.10.DEMB10ES002.KC473842
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+>B.ES.10.R3.KT200352
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+>B.ES.10.R4.KT200353
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+>B.ES.10.R6.KT200355
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+>B.ES.10.R7.KT200356
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+>B.ES.10.R8.KT200357
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+>B.ES.13.DEMB13ES010.KP109518
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+>B.ES.13.P6.KT200348
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+>B.ES.89.U61.DQ854716
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+>B.FR.03.LA06ToXa.KU168261
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+>B.FR.08.DEMB08FR002.JX140654
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+>B.FR.09.DEMB09FR001.KF716494
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+>B.FR.09.DEMB09FR002.KF716495
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+>B.FR.11.DEMB11FR001.KF716496
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+>B.GB.08.DEMB08UK003.KY658697
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+>B.GW.14.DEMB14GW004.MH078546
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+>B.IN.x.11807.EF694037
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+>B.JP.00.DR2508.AB289588
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+>B.JP.01.DR388.AB289590
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+>B.JP.02.197.AB428554
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+>B.JP.04.04JPDR6075B.AB221125
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+>B.JP.04.DR5913.AB480696
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+>B.JP.04.DR6089.AB286955
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+>B.JP.04.DR6175.AB480694
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+>B.JP.05.DR6538.AB287363
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+>B.JP.05.DR6737.AB287364
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+>B.JP.05.DR7060.AB287366
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+>B.JP.05.DR7065.AB287368
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+>B.JP.08.NMC104_clone_01.AB731663
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+>B.JP.09.NMC127_clone_07.AB731667
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+>B.JP.11.DEMB11JP002.KF716497
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+>B.JP.11.NMC851C_clone_13.AB731669
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+>B.JP.12.DEMB12JP001.KF716498
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+>B.JP.98.DR1120.AB480698
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+>B.JP.99.DR1348.AB287370
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+>B.JP.x.DR1673.AB564745
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+>B.JP.x.DR1712.AB604946
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+>B.JP.x.JRC03B.AB565496
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+>B.JP.x.JRC05B.AB565497
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+>B.JP.x.JRC65B.AB565502
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+>B.JP.x.pJPDR0796B02.AB565478
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+>B.KR.02.HP_19_02LGS11_3443.KJ140264
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+>B.KR.02.HP_20_02KJO10_3480.KJ140265
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+>B.KR.03.03HJY8.JQ316131
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+>B.KR.03.03KDE11.JQ316128
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aagaactgctga-----------------------------------catcgagcttt------------ctac---aa--gggactttcc-------------------gct--ggggacttacca--ggg-aggcgtggc--------------ctggg-cgggact-gggg-agtggc-gag-ccctcaga-tgctgcataaaagcag-ctgctttctgcctgtact-g-ggtctctc--tggttagaccagatc-t-gagcctgggagctctctgg-ctaac-taggg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-ttt--aa-g-----ta-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccctt-ttag-t-cagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------gcgaaagcgaaag------------------------------------------tagaaccggagga--------gctctcttgacgca-ggactcggcttgct---gaagcgcgcacggcaagaggc-------------gagg-gg--cggc-----gaccggtgagtacgcc--------------------------aatttttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggagaattagatagatgggaaaaaattcggtta---agg------cca---gggggaaagaaaaaatataggttaaaacatatagtatgggcaagcagggagctagaacgattcgcagttaatcctggcctgctagaaacatcagaaggctgtagacaaatattgggacagctacaaccagcc---cttcagacaggatcagaagaaattaaatccttatttaatacagta---gcaaccctctattgtgtacatcaaaggatagagataaaagacaccaaggaagctttagagaagatagaggaagagcaaaacaaaagtaag------------------------aaaaaggcacagcaagcaacagct---------------------ggcacagga------------------aac---agcagtcag------------------------gtcagccaaaattaccctata------------gtgcagaacctccaggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgggtaaaagtagtagaagagaag------gctttcagcccagaagtaatacccatgttttcagcattctcagaaggagccaccccacaagatttaaacaccatgctaaacacagtggggggacatcaa---gcagctatgcaaatg---ttaaaagag---accatcaatgaggaagctgcagaatgggatagattgcat---ccagtgcatgca---gggcctattgcaccaggccagatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaataggatggatgaca---------aataatcca---cct---atc---ccagta---ggagaaatctataaaagatggataatcctgggattaaataaaatagtaagaatgtatagccctaccagcattctggacataaaacaaggaccaaaggaaccctttagagactatgtagaccggttctataaaactctaagagccgagcaagcgtcacaggaggtaaaaaattggatgacagaaaccttgttggtccaaaatgcaaacccagattgtaagactattttaaaagcattgggaccagcagctacactagaagaaatgatgacagcatgtcagggagtgggaggacccggccataaa---gcaagagttttggctgaa------gcaatg---agccaagtaacaaat---------------------tcagctaccata---atgatg------cagagaggcaat---------ttc---aggaaccaaagaaaa------cctgttaagtgtttcaattgtggcaaagaaggg---cacatagccaaaaattgcagggcccctaggaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagattgt---------------actgagagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagagcagaccagagccatcagc------------------------------------------------------cccaccaga------agagagcttcaggtt------------tggggaagagacaacaac---tccctc------------------------------tcagaa---------------gcaggagcc------------gatagacaa---------------------------gga------------actgta------tcctttagcttccctcagatcactctttggcaacgacccctcgtcacaataaaagtaggggggcaactaaaggaagctctattagatacaggagcagatgatacagtatta---gaagaa---atgaatttaccagggagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcagataaccatagaaatctgtggacataaagctataggtacagtattagtaggacctacacctgtcaac---ataattggaagaaatctgttgactcagattggctgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaggcattagtagaaatttgtaca------gaaatggaaaaggaaggaaaaatttcaaaa---attgggcct---gagaatccatataatactccagtatttgccataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctgggaa---gttcaa------tta---ggaata---------------------------ccacatccagcagggttaaaaaagaaa---aaa------tcagtaacagtactggatgtgggtgatgcatat---ttttcagttcccttagatgaagacttcagaaagtatactgcatttaccatacctagtttaaacaatgagacaccagggattagatatcagtacaatgtgcttccacaggggtggaaaggatcaccagcgatattccaaagtagcatgacaaaaatcttagagccttttagaaaacaaaatccagacatagttatctatcaatacatggatgatttgtatgtaggatctgacttagaaatagggcagcatagactaaaaatagaggaactgagacaacatctgttgaagtggggatttaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctataatgctaccagaa---aaagac---agctggactgtcaatgacatacagaagttagtgggaaaactgaattgggcaagtcagatttatgcaggaattaaagtaaagcaattatgcaaactccttaggggaaccaaggcactaacagaagtagtaccactaacagaagaagcagagctagaactggcagaaaacagggaaattctaaaagaaccagtacatggagtgtattatgacccatcaaaagacttaatagcagaaatacagaagcaggggcaaggccaatggacatatcaaatttatcaagacccatttaaaaatctgaaaacaggaaagtatgcaagaatg---aggggtgcccacactaatgatgta------aagcaattaacagaggcagtgcaaaaaatagccatggaaagcatagtaatatggggaagg---actcctaaatttagactacccatacagaaagaaacatgggaagcatggtggacagagtattggcaagccacttggattcctgagtgggagtttgtcaatacccctcccttagtgaaattatggtaccagttagaaaaagaacccatagtaggagcagagactttctatgtagatggggcagctaatagagaaactaaatcaggaaaagcaggatatgttactgacagaggaagacaaaag---gttgtctccctaacggacacaacaaatcagaagactgagttacaagcaattcatctagctttgcaggattcaggattagaag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+>B.KR.03.03KGS5.JQ316132
+---------------------------------------------------------------------------------------------------gggccaggg-atcagatatccaataacctttgggtggtgcttcaagctagtgccagtagagccagaaaaggtagaagag--gcc---actgcaggagagagcaactgcttgttacaccccataaacctgcatggaatggatgacccggagggagaagtgttagtgtggaagtttgacagccacctagcattt---catcacatggcccgagagaaa------cat--ccggagtac------------------------tacaagaactgctga-------------------catcgagaactgctgacagcgagcttt------------ctac---aa--gggactttcc-------------------gct--ggggactttccg-tggg-aggcgtggc--------------ctggg-cgggact-gggg-agtggc-gag-ccctcaga-tgctgcataaaagcag-ctgctttttgcctgtact-g-ggtctctc--tggttagaccagatc-t-gagcctgggagctctctgg-ctagc-tgggg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-ttc--aa-g-----ta-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagacc-tt-ttag-t-cagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------cagaaagcgaaag------------------------------------------tagaaccggagga--------gctctctcgacgca-ggactcggcttgct--gaaagcgcgcaccacaagaggc-------------gagg-gg--cggc-----gactggtgagtacccc------------------------aaattttttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagcgggggaaaattagatcaatgggaaaaaattcggtta---agg------cca---ggaggaaagaaaaaatatcagttaaaacatctagtatgggcaagcagggagctagaacgattcgcagttaatcctggcctgttagaaacagcagaaggctgtagacaaatattgggacagctacaaccatcc---cttcagacaggatcagaagaacttaaatcattatataatgcagta---gcaaccctctattgtgtacatgaaaggatagagataaaagacaccaaggaagctttagataagatagaggaagagcaaaacaaaatgaag------------------------aaaaaggcacagcaagcaacagct---------------------gacacagga------------------aac---agcagccag------------------------gtcagccaaaattaccctata------------gtgcagaacctccaggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgggtaaaagtaatagaagagaag------gctttcagcccagaggtaatacccatgttttcagcattatcagaaggagccaccccacaagatttaaacaccatgttaaacacagtggggggacatcaa---gcagctatgcaaatg---ttaaaagag---accatcaatgaggaagctgcagaatgggatagattgcat---ccagtgcatgca---gggcctattgcaccaggccagata---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggagcaaatactatggatgaca---------aataatcct---cct---atc---ccagta---ggagaaatctataaaagatggataatcctggggctaaataaaatagtaagaatgtatagccctaccagcattctggacataagacaaggaccaaaggaaccctttagagattatgtagacaggttctataaaactctaagagccgagcaagcatcacaggaggtaaaaaattggatgacagaaaccttgttggtccaaaatgcaaacccagattgtaagactattttgaaagcactgggaccaggagctacactagaagaaatgatgacagcatgtcagggagtgggaggacccggccataaa---gcaagagttttagctgaa------gcaatg---agccaagtaacaaat---------------------tcagctaccata---atgatg------cagagaggcaat---------ttc---aggaaccaaagaaag------attgttaagtgtttcaattgtggcagagaaggg---cacatagccaaaaattgcaaggcccctaggaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagattgt---------------actgagagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---aag---gccagggaattttcctcagagcagactagagccaacagc------------------------------------------------------cccaccaga------agagagcttcaggtt------------tggggaagagacaacaac---tccctc------------------------------tcagaa---------------gcaggagcc------------gatagacaa---------------------------gga------------actgta------tccttcagcttccctcaaatcactctttggcaacgacccctcgtcacaataaagataggggggcaactaaaggaagctctattagatacaggagcagatgatacagtatta---gaagaa---atgagtttaccagggagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcagatagccatagaaatctgtggacataaagctataggtacagtattagtaggacctacacctgtcaac---ataattggaagaaatctgttgactcagattggctgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaggcattagtagaaatttgtaca------gaaatggaaaaggaaggaaaaatttcaaaa---attgggcct---gaaaatccatataatactccagtatttgccataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctgggaa---gttcaa------tta---ggaata---------------------------ccacatccagcagggttaaaaaagaaa---aaa------tcagtaacagtacgggatgtgggtgatgcatat---ttctcagttcccttagatgaagacttcaggaagtatactgcatttaccatacctagtataaacaatgagacaccagggattagatatcactacaatgtgcttccacaggggtggaagggatcaccagcgatattccaaagtagcatgacaaaaatgttagagccttttagaaaacaaaatccagacatagtcatctatcaatacatggatgatttatatgtaggatctgacttagaaatagggcagcatagaataaaaatagaggaagtgagacaacatctgttgaagtggggatttaccacaccagacaagaaacatcggaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctataatgctaccagaa---aaggac---agctggactgtcaatgacatacagaagttagtgggaaaactgaattgggcaagtcagatttatgcaggaattaaagtaaagcaattatgtaaactccttaggggaaccaaagcactaacagaagtagtaccactaacagaagaagcagagctagaactggcagaaaacagggaaattctaaaacaaccagtacatggagtgtattatgacccatcaaaagacttaatagcagaaatacagaagcaggggcaaagccaatggacatatcaaatttatcaagagccatttaaaaacctgaaaacaggaaaatatgcaagaatg---aggagtgctcacactaatgatgta------aaacagttaacagaggtcgtgcaaaaggtaaccacagaaagcatagtaatatggggaaag---actcctaaatttaaactacccatacaaaaggaaacatgggaagcatggtggacagagtattggcaagccacttggattcctgagtgggagtttgtcaatacccctcccttagtgaaattatggtaccagttagaaaaagaacccatagtaggagcagaaactttctatgtagatggggcagctaatagggaaactaaattaggaaaagcaggatatgttactgacagaggaagacaaaag---gttgttcccctaacggacacaacaaatcagaaaactgagttacaagcaattcatctagctttgcaggattcaggattagaag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+>B.KR.04.04CWS5.JQ316133
+----------------------------------------------tgtggatctaccacacacaaggctacttccctgattggcagaactacacaccagggccaggg-atcagatatccactgacctttgggtggtgcttcaagttagtaccagttgatccagaaaagatagaagag--gcc---actgtaggagagaacaactgcttgttacaccccctgaaccagcatggaatggatgacccagagagagaagtgttgatgtggaagtttgacagccgcctggcattt---catcacatagcccgagagcta------cat--ccggagtac------------------------tacaaggactgctga-----------------------------------catcgagcttt------------ctac---aa--gggactttcc-------------------gct--ggggactttccgcaggg-aggcgtgga--------------ctggg-cgggact-gggg-agtggc-gaa-ccctcaga-tgctgcataaaagcag-ctgctttctgcctgtact-g-ggtctctc--tggttagaccagatc-c-gagcctgggagctctctgg-ctgac-taggg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-ttt--aa-g-----ta-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccctt-ttag-t-cagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ccgaaaacgaaag------------------------------------------tagaaccagagga--------gctctctcgacgca-ggactcggcttgct---gaagcgcgcacagcaagaggc-------------gaga-gg--cggc-----gactggtgagtacgcc------------------------gaaatttttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcgatattaagcgggggaaaattagaccaatgggaaaaaattcggtta---agg------cca---gggggaaagaaaaaatataggttaaaacatctagtatgggcaagcagggagctagaacgatacgcagttaaccctggtcctgttgaaacaccagaaggctgtagacagatattgggacagctacaaccagcc---cttcagacaggatcagaagaacttaaatcattatataatacagta---gcaaccctctattgtgtacatcaaaggatagagataagagacaccaaggaagctttagagaggatagaggaagagcaaaacaaaagtaag------------------------aaaaaggcacagcaagcaacagct---------------------gacacagga------------------aac---agcagccag------------------------gtcagccaaaattaccctata------------gtgcagaaccttcaggggcaaatggtacatcagcccatatcacctagaactttaaatgcatgggtaaaagtaatagaagagaag------gcttttagcccagaagtaatacccatgttttcagcattatcagaaggagccaccccacaagatttaaacaccatgctaaacacagtggggggacatcaa---gcagctatgcaaatg---ttaaaagag---accatcaatgaggaagctgcagaatgggataggttgcat---ccagcgcaggca---gggcctgttgcaccaggccagata---agagacccaaggggaagtgacatagcaggaactactagtacc---cttcaggagcaaataacatggatgaca---------aataatcca---tct---atc---ccagta---ggagaaatctataaaagatggataatcttgggattaaataaaatagtaagaatgtatagccctatcagcattctggacataagacaaggaccaaaggaaccctttagagattatgtagaccggttctataaaactctaagagctgagcaagcgtcacaagaggtaaaaaattggatgacagaaaccttgttggtccaaaatgcaaacccagattgtaaaactattttaaaagcattgggaccagcagcttcactagaagaaatgatgacagcatgtcagggagtgggaggacccggccataaa---gcaagagttttggctgaa------gcaatg---agccaaatgacaaat---------------------tcagctaccata---atgatg------caaagaggcaat---------ttc---aggaaccaaagaaaa------actattaagtgtttcaattgtggcaaggaaggg---cacctagccaaaaattgcagggcccctaggaaaaaaggctgttggaaatgtggaaaggaaggacaccaaatgaaagattgt---------------aatgagagacaggccaattttttagggagaatctggcc---ttcccacaa------ggg---aag---gccagggaattttcttcagagcagaccagagccatcggc------------------------------------------------------cccaccaga------ggagagcttcaggtt------------tggggaggagacaacaac---tccccc------------------------------tcagaa---------------gcaggagcc------------gatggacaa---------------------------gga------------cctgta------tcctttagcttccctcagatcactctttggcaacgacccctcgtcacaataaagataggggggcaactaaaggaagctctgttagatacaggagcagatgatacagtatta---gaagaa---atgagtttaccagggagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcaggtaaacatagaaatctgtggacataaagctacaggtacagtattagtaggacctacacctgtcaac---ataattggaagaaatctgttgactcagattggctgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaggcattagtagaaatttgtaca------gaaatggaaaaggaaggaaaaatttcaaaa---attgggcct---gaaaatccatataatactccagtatttgccataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctgggaa---gttcaa------tta---ggaata---------------------------ccacatccagcagggttaaaaaggaaa---aaa------tcagtaacagtactggatgtgggtgatgcatat---ttttcagttcccttagataaagacttcaggaagtatactgcatttaccatacctagcataaacaatgagacaccagggattagatatcagtacaatgtgcttccacaggggtggaaaggatcaccagcgatattccaaagtagcatgacaaaaatcttagagccttttagaaaacaaaatccagatgtagttatctaccaatacatggatgatttatatgtaggatctgacttagaaatagggcagcatagaataaaaatagaggaactgagacaacatctgttgaagtggggatttaccacaccagacaaaaaacatcagaaagaacctccatttctttggatgggttatgaactccatcctgataaatggacagtacagcctataatgctaccagaa---aaagac---agctggactgtcaatgacatacagaagttagtgggaaaactgaattgggcaagtcagatttatgcagggattaaggtaaagcaattatgtaaactccttaggggaaccaagtcactaacagaagtagtgccactaacagaagaagcagagctagaactggcagaaaacagggaaattctgaaagtaccagtacatggagtatattatgacccatcaaaagacttaatagcagaaatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatgcaagaatg---aggggtgcccacactaatgatgta------aaacaattaacagaggcagtgcaaaaaatagccatagaaagcatagtaatatggggaaag---actcctaagtttaaactacccatacaaaaagaaacatgggaagcatggtggacagagtattggcaagccacttggattcctgagtgggagtttgtcaatacccctcccttagtgaaattatggtaccagttagaaaaggaacctatagtaggagcagaaactttctatgtagatggggcagctaatagggacactaaattaggaaaagcaggatatgttactgacagaggaagacaaaag---gttgtccccctaacggacacaacaaatcagaagactgagttacaagcaattcatctagctttgcaggattcaggattagaag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+>B.KR.04.04KJS8.JQ316130
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+>B.KR.04.04KMK5.JQ316126
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+>B.KR.04.04LHS6.AY839827
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+>B.KR.04.HP_2_04JJW2a.MT679550
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+>B.KR.05.05CSR3.DQ837381
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+>B.KR.05.05YJN2.JQ316134
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+>B.KR.07.07KTG10_HP_14.MN043605
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+>B.KR.07.07KYY4.JQ341411
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+>B.KR.12.12Lsw3_HP_15.MT224127
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+>B.KR.19.HP_7_19LSM8_Aug_2019A.MT559052
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+>B.KR.91.91OSG10.KF561442
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+>B.KR.92.HP_10_02SHJ8_6986.KJ140255
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+>B.KR.93.93BGO2_Feb_1993.MT559045
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+>B.KR.93.93JJS10.MK577479
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+>B.KR.93.93KJK4.MN237645
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+>B.KR.93.93PJA9.MN043595
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+>B.KR.93.HP_17_02LSP11_2268.KJ140262
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+>B.MM.99.mSTD101.AB097870
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+>B.NL.86.3202A21_ACH3202A21.U34604
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+>B.PE.06.502_0524_FL04.JF320008
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+>B.PE.06.502_0841_FL04.JF320208
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+>B.PE.06.502_2794_FL05.JF320244
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+>B.PE.07.502_2622_wg1.JF320189
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+>B.PE.13.DEMB13PE010.MH078552
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+>B.PE.14.DEMB14PE012.MN703133
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+>B.PE.16.DEMB16PE009.MH078555
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+>B.PH.15.DEMB15PH002.KY658689
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+>B.PH.15.DEMB15PH003.KY658690
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+>B.PH.16.1022.MH327757
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+>B.RU.09.09RU4457.JX500709
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+>B.RU.11.11RU21n.JX500708
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+>B.SE.03.003SE.MF373125
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+>B.SE.03.005SE.MF373127
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+>B.SI.11.Sample29_SI257.MN736700
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+>B.SI.15.Sample56_SI457.MN736706
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------g-cctac-taggg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-ttc--aa-g-----ta-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------tctagagatc-------cctcagaccatt-ttag-t-cagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------agaaaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcgcacagcaagaggc-------------gagg-cg--cggc-----gaccggtgagtacgcc----------------------agaaaatttttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggaaaattagatagatgggaaaaaattcggtta---agg------cca---gggggaaagaaaaagtataaattaaaacatatagtatgggcaagcagggagctagaacgattcgcagttaatcctggcctgttagaaacatcagaaggctgtagacaaatactagcacagctacaaccttcc---cttcagacaggatcagaagagcttaagtcattatataacacagta---gcaaccctctattgtgtacatcaaaacatagagataaaagacaccaaggaagctttagagaagatagaggaagagcaaaacaaaagtaag------------------------aaaagggcacagcaagcagcagca---------------gcagctgacacagga------------------------agcagccag---------------------caggtcagccaaaattaccctata------------gtacagaacctacaggggcaaatggtacatcagtccatatcacctaggactttaaatgcatgggtaaaagtaatagaagagaag------gccttcagcccagaagtaatacccatgttttcagcattgtcagaaggagcaaccccacaagatttaaacaccatgctaaacacagtggggggacatcaa---gcagctatgcaaatg---ttaaaagag---accatcaatgaggaagctgcagaatgggatagaatgcat---ccaccacaggca---gggcctattgcaccaggccagata---agagaaccgaggggaagtgatatagcaggaactactagtacc---ctccaggaacaaataacatggatgaca---------agtaatcca---cct---gtc---ccagta---ggagaaatctataaaagatggataatcttgggattaaataaaatagtaaggatgtatagcccagtcagcatcctggacataaaacagggaccaaaagaaccttttagagattatgtagaccggttctataaaactttaagagccgagcaagcttcacaagaggtaaaaaattggatgacagaaagtttgttggtccaaaatgcgaatccagattgcaaaactattttaaaagcattaggaccagcagctacattagaagaaatgatgacagcatgtcagggagtggggggacccagccataaa---gcaagagttttggctgaa------gcaatg---agccaagcaacaggt---------------------gcagctaccata---atgatg------cagaaaggcaat---------ttt---aagaatcaaaggaaa------actgttaaatgtttcaattgtggcaaagaaggg---cacatagccagaaattgcagggcccctagaaaaaagggctgttggaaatgtgggagggaaggacaccaaatgaaggattgc---------------actgagagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---aag---gccagggaactttctccagagcaggccagaaccaacagt---------------------------------------------gccaacagccccaccaga------ggagagcttcaggtt------------cggggaggagatgacagc---tccccc------------------------------tccgaa---------------gcaggaacc------------gca---------------------------------gga------------gctata------tcctgtaacctccctcagatcactctttggcaacgacccctcgtcacaataaagatagggggacaattaaaggaagctctattagatacaggagcagatgacacagtagta---gaagaa---atgaatttgtcaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcaggtacccatagaaatctgtgggcataaagctataggtacagtattagtaggacctacacctgtcaac---ataattggaagaaatctgttgacccaaattggttgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaggcattaatggagatttgtaca------gaaatggaaaaggaagggaaaatttcaaaa---attgggcct---gaaaatccatacaatactccaatatttgccataaagaaaaaagacagt------actaaatggagaaaattggtagatttcagagaacttaataagagaactcaagacttctgggaa---attcaa------tta---ggaata---------------------------ccacatccttcggggttaaaaaagaaa---aaa------tcagtaacagtcctggatgtgggtgatgcatat---ttttcagttcccttagatgaggactttagaaagtatactgcatttactatacctagtataaacaatgaaacaccaggaattagatatcagtacaatgtacttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatcttagagccttttagaaaacaaaatccagagatggttatctatcaatacatggatgatttgtatgtaggatctgacttagaaatagggcagcatagagaaaaaatagagaaactgagacaacatttgttgaagtggggatttaccaccccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccagag---aaagac---agctggactgtcaatgacatacagaagttagtgggaaaattaaattgggcaagtcagatttacccagggattaaagtaaagcaattatgtaagctccttaggggaaccaaagcactaacagaagtagtaccactaacagaagaagcagagcttgaactagcagagaacagggaaattctaaaggaaccagtacatggagtgtattatgacccatcaaaagacttaatagcagagttacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaagtatgcaagaatg---aggggtgcccacactaatgatata------aaacaattaacagaggcagtgcaaaaaatagctcaagaaagcatagtaatatggggaaag---acccctaaatttaaattacccatacagaaggaaacatgggaagcatggtggatggagtattggcaagccacctggattcctgagtgggaatttgtcaatacccctcccctagtaaaattatggtatcagttagaaaaagaacccatagcaggagcagaaaccttctatgtagatggggcagctaatagggaaactagaataggaaaagcaggatatgttactgacagaggaagacaaaag---gttgtccccttacctgacacaacaaatcagaagactgagctacaagcaatttatctagcgttacaggactcagggctagaag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+>B.SI.16.Sample12_SI159.MN736698
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------g-ctagc-taggg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-ttc--aa-g-----ta-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagactatt-ttag-t-cagtgtgaaaaa-tctctagcagtggcg--------cccgaacagggac------------------cgtgaaagtgaaa------------------------------------------gtgaaccagagga------gctctctcgacgcaaa-ggactcggcttgct---g-agcgcgcacagcaagaggc-------------gagg-gg--cggc-----gactggtgagtacgcc-------------------------aaatttttgact----------agcaga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagtgcgggggaattagatagatgggaaaaaattcggtta---agg------cca---gggggaaagaaaaaatataggttaaaacatatagtatgggcaagcagggagctagaacgattcgcagtcaatcctggcctgttagaaacatcagaaggctgcagacaaatactgggacagttacaatcatcc---cttcagacaggatcagaagaacttagatcattatataatacagta---gcaacactctattgtgtgcaccaaaagatagagataaaagataccaaggaagctttagataagatagaggaagagcaaaacaaaagcaag------------------------acaagagcacagcaagcagcagct---------------------gacacagga------------------aaa---aacagccag------------------------gtcagccaaaattaccctata------------gtacagaaccaccaggggcaaatggtacatcagcctatatctcctagaactttaaatgcatgggtaaaagtagtagaggagaag------gcttttagcccagaagtaatacccatgttttcagcactatcagaaggagccaccccacaagatttaaacaccatgctaaacacagtggggggacaccaa---gcagccatgcaaatg---ttaaaagag---accatcaatgaggaagctgcagaatgggatagattgcat---ccagtgcaggca---ggacctgttgcaccaggtcagctg---agagaaccaaggggaagtgacatagcaggaagtactagcagt---cttcaggaacaaatagcatggatgaca---------cacaatcca---cct---atc---ccagta---ggagaaatctataagagatggataatcctgggattaaataaaatagtaagaatgtatagtcctaccagcattctagatataaaacaagggccaaaagaaccttttagagattatgtagaccggttctataaaactctaagagccgagcaagcttcacaggaggtaaaaaattggatgacagaaaccttgttggtccaaaatgcgaatccagattgtaaaactcttctaaaagcattgggaccaggagctacattagaagaaatgatgacagcatgtcagggagtagggggacccggccataaa---gcaagagttttggctgaa------gcaatg---agccaagcaacaagt------------------gcagccaccatgatg---atgatg------cagaaaggcaat---------ttt---aggaaccaaagaaaa------actgttaagtgtttcaattgtggcaaagaaggg---cacgtagccagaaattgcagggcccctaggaaaaagggctgttggaaatgtggaagagaaggacaccaaatgaaagattgc---------------actgagagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---aag---gccagggaatttccttcagaacagaccagagccaacagc---------------------------------------------cccaccagccccaccaga------agagagcttcaggtt------------tggggaagcaac---agc---tccctctcagaa------------gcaggaaccgactcagaa---------------gcaggagcc------------gatagacaa---------------------------gga------------actgta------tcctttagcttccctcagatcactctttggcaacgacccctcgtcacaataaagatagggggacagctaaaggaagctctattagatacaggagcagatgatacagtatta---gaagaa---atgtctttgccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcagataacagtagaaatctgtggacataaagctataggtacagtattaataggacctacacctgtcaac---ataattggaagaaatctgttgactcagattggttgcactctaaattttcccattagtcctattgaaactgtaccagtgaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaggcattagtagaaatttgtaca------gaaatggaaaaggaagggaaaatttcaaaa---attgggcct---gaaaacccatacaatactccagtatttgccataaagaaaaaagatggt------actaaatggagaaaattggtagatttcagagaacttaataaaagaactcaagacttctgggaa---gttcaa------tta---ggaata---------------------------ccacatcctgcagggttaaaaaagaaa---aaa------tcagtaacagtcctggatgtgggtgatgcatat---ttttcagttcccttagataaagagtttagaaagtatactgcatttaccatacctagtataaataatgagacaccaggaattagatatcagtacaatgtgctgccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatcttggaaccttttagaaaacaaaatccagaaatggttatctatcaatacatggatgatttgtatgtaggatctgacttagaaatagggcagcatagaacaaaaatagaggaactgagacaacatctgttgaagtggggatttaccacaccagacaaaaaacatcagaaagaacctccattctcttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccagac---aaagac---agctggactgtcaatgacatacagaaattagtgggaaaattgaattgggcaagtcaaatttatccagggattaaagtaaagcaattatgtaggctccttaggggaaccaaagcactaacagaagtagtaccactgacagaagaagcagagctggaactagcagaaaacagggagattctaaaagaaccagtacatggagcgtattatgacccatcaaaagacttaatagcagacatacagaagcaggggcaaggtcaatggacatatcaaatttatcaagagccatataaaaatctgaaaacaggaaaatatgcaagggtg---aagggtgcccacactaatgatata------aagcagttaactgaagcagttcaaaaaatagccatagaaagcatagtaatatggggaaag---actcctaaatttagactacccatacaaaaggaaacatgggaagcatggtggatggactattggcaagccacctggattcctgagtgggaatttgtcaatactcctcctctagtaaaattatggtatcagttagaaagagaccctataataggagcagaaactttctatgtagatggggcagctaatagggagactaaattaggaagagcaggatatgttactgacagaggaagacaaaag---gttgtcaacctaacagacacaacaaatcagaagactgagttacaagcaattcatctagcattgcaggattcgggactagaag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+>B.SI.16.Sample65_SI497.MN736707
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+>B.TH.04.04TH601066.JN248329
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+>B.TH.04.04TH821921.JN248337
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+>B.TH.05.05TH357801.JN248346
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+>B.TH.05.05TH429730.JN248347
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+>B.TH.10.DEMB10TH002.KP109514
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+>B.TH.13.2544072P000FL_Sd.MG989506
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+>B.US.00.929172.KT124806
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+>B.US.00.ES1_20.EF363123
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+>B.US.00.RHPA_TF1.JN944917
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tcttaggagcagca---ggaagcactatgggcgcagcgtca---ataacgctgacggtacaggcc---aga------cta---ctattg---tctggtatagtgcaacagcag---agcaatctg---ctgagggctattgaggcgcaacagcatctgttgcaactcacagtctggggcatcaagcagctccag---gcaagagtcctggctgtggaaagatacctaaaggatcaacagctcctggggatttggggttgctctggaaaactcatctgcaccactgctgtgccttggaatgct---agt---tgg------------------------------------agtaataaatctcaggatacgatttgg---------gga---aacatgacttggatgcag---tgg---gaa-agagaaattgacaattacacagacttaatctacaacttacttgaagaatcgcag-aaccaacaagag-aaaaatgaacaagaattattggcattggataaatgggcaagtttgtggagttggtttagcataacacactggctgtggtatata-aaaatgttcataatgatagtaggaggcttggtaggttta-agaatagtttttgctgtactttctatagtgaatagagttaggcagggatactcaccattatcg---tttcag---acccgcttcccagcc------ccgagggga------cccgacagg------cccgaaggaatcgaagaagaaggtggagagcgagacagagacagatcagggagatcagcagatggattcttagtactcgtctgggtcgatctgcggaacctttgcctcttcagctac---caccgcttgagagacttactcttgattgtaacgaggactgtggaa---ctt---ctg---ggacgc---------------------------------------------agggggtgg------gaagccctcaaa---tattgg---------tggaatctcctacagtattggagccaggaactaaagaagagtgct--gttagtttgcttgatgccatagccatagcagtagctgag-ggaacagataggattatagaactattacaaagaatttttaga------gcttttctccacatacctaca---agaataagacagggcttggaaagggca------ttg-------caa---taa--------------------------------------gatgggtggcaagtggtcaaaa------cgtagtgca---ggt---ggatggtctactgtaagagaaaaaataagacgagct------------------------------------------------------------gagccagca------------------------------gcagatggggtgggagca---gtatctcgagacctggaaaaacatggagcaatcacaagtagcaataccgcagctactaatgctgat---tgtgcctggctagaagca---------caagaggac---------gag------gaggtgggttttccagtcagacctcaggtgcctctaagaccaatgacatacaaggcagctgta------gatcttagccactttttaaaagaacaggggggactg---gaagggttagttcactcccagagaagacaagatatc---------cttgatctatggatttaccacaca-caa---ggctacttccctgattggcag---aattacacaccagggccaggggtcagatatccactgacctttggatggtgcttcaagctagtaccagttgagccagataaggtagaagaa------gccaatgaagga------gagaataacagcttgttacaccctctgagccagcatgggatggatgacccg---gagaaa---gaagtgttagtgtggaagtttgacagccgcctagca-tttaatcacgtggcccgagagctgcat---ccggactac------------------------tacaagaactgctgac-----------------------------------------atcgagctt-------------------------tctacaa----------------------------------------gggactttcc----------------gctg---------------------------------------gggactttcc---------------------------------------------------------------------------------agggaggc------------gtggac-tgggcgggact-----------gggg-agtg-gc-gagccc--tcag-a-----tgctgcat--ataagcag-c-tgcttttt-gc-c-tg-ta--ctgg-g----tc-tctc-ta--------g-ttag----a--ccagat---------------------------------------------------------------------ctgag---------------cc-tggg-agctc--------tctgg-----------c------tagc-t-agggaac-ccactgctt--aa-gcct----c-aat--aaagc-ttgc---c-----------tt--ga--g-tgct-ttaag-tagtgtgtgcccgtctg-t--tgt-------------gt-gact-c--------------tggt-aact-agaga-tccctcagac-ct----t-tt-------agtcagtgtggaaa--atctctagca------------------------------------------------------------------------------
+>B.US.00.THRO_TF1.JN944930
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+>B.US.01.L805.FJ469738
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+>B.US.01.REJO_TF1.JN944911
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+>B.US.02.328659.KT124764
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+>B.US.02.996401.KT124814
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+>B.US.02.CR0023W.FJ469688
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+>B.US.02.CR0058S.FJ469693
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+>B.US.02.F706.FJ469728
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+>B.US.02.F714.FJ469730
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+>B.US.02.F719.FJ469734
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+>B.US.02.F762P.FJ469735
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+>B.US.02.F797.FJ469737
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+>B.US.02.HIV_US_BID_V5249_2002.JQ403102
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+>B.US.02.HIV_US_BID_V5276_2002.JQ403105
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+>B.US.02.L8124P.FJ469741
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+>B.US.02.L893P.FJ469749
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+>B.US.02.PRLS08.FJ469757
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+>B.US.02.PRLS09.FJ469758
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+>B.US.02.PRLS16.FJ469760
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+>B.US.03.933384.KT124807
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+>B.US.03.AT01480.FJ469686
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+>B.US.03.CR0154X.FJ469701
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+>B.US.03.DEMB03JP004.KC473846
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+>B.US.03.F7157.FJ469731
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+>B.US.03.L8107.FJ469739
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+>B.US.03.L8116.FJ469740
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+>B.US.03.L8152.FJ469742
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagcgggggacaattagatagatgggaaaaaattcgatta---agg------cca---ggaggaaagaaacaatacaaactaaaacatctagtatgggcaagcagggagctagaacgattctcaattaatcctggcctgttagaaaccgcagaaggttgtagacaaatactgagacagctacaaccatcc---cttcagacaggatcagaagaacttaaatcattatttaatacagta---gcaaccctctattgtgtgcatcaaaggatagatgtaaaagacaccaaagaagctttagataagatagaggaagaacaaaacaaaagtaag------------------------aaaaaggcacaacaagcagcagca------------------gctgacacagaa------------------aat---agcagccag------------------------gtcagccaaaattaccccata------------gtgcagaacgtgcaggggcaaatggtacatcaggctatatcacctagaactctaaatgcatgggtaaaagtagtagaagagaag------gctttcagcccagaagtaatacccatgttttcagcattatcagaaggagccaccccacaagatttaaacaccatgctaaacacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagag---accatcaatgaggaggctgcagaatgggatagattgcat---ccagtgcatgca---gggcctattgcaccaggccagatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaataggatggatgaca---------cataatcca---ccc---atc---ccagta---ggagaaatttataaaagatggataatcatgggactaaataaaatagtaagaatgtatagccctactagcattctggacataagacaaggaccaaaggaaccctttagagactatgtagaccggttctataaaactctaagagccgagcaagcttcacaggaggtaaaaaattggatgacagaaactttgttggtccaaaattcgaacccagattgtaaaactattctaaaagcattgggaccaggggcctcactagaagaaatgatgacagcatgtcagggagtgggaggacccagccataaa---gcaagaattttggctgaa------gcaatg---agccaagtaacaaat---------------------ccagctaccata---atgata------cagaaaggcaat---------ttt---aggaaccaaagaaag------cctgttaagtgcttcaattgtggcaaagaaggg---cacgtagccagaaattgcaaggcccctaggaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagattgt---------------actgagagacaggctaattttttagggagaatctggcc---ttcccacaa------ggg---aag---gccagggaattttcttcagagcagaccagagccatcagc------------------------------------------------------cccaccaga------agagagcttcaggtt------------tgtggaggagacaacaac---tccctc------------------------------tcagaa---------------gcaggacac------------gatagagaa---------------------------aga------------aacgta------tcctttagcttccctcaaatcactctttggcaacgacccctcgtcacaataaagatagggggacagctaaaggaagctctattagatacaggagcagatgatacagtatta---gaagat---ataaatttgccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaaaacagtat---gatcagataactgtagacatctgtggacataaagctacaggtacagtattagtaggacctacacctgtcaac---ataattggaagaaacctgttgactcaaattggttgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaagcattagtagaaatttgtaca------gaaatggaaaaggaaggaaaaatttcaaaa---attgggcct---gaaaatccatacaatactccagtatttgccataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttttgggaa---gttcaa------tta---ggaata---------------------------ccacatccctcagggttaaaaaagaaa---aaa------tcagtaacagtactagatgtgggtgatgcatat---ttttcagttcccttagataaggacttcaggaagtatactgcatttaccatacctagtgtaaacaatgagacaccagggattagatatcagtacaatgtgcttccccagggatggaaaggatcaccagcaatattccaagctagcatgacaaaaattttagagccttttagaaagcaaaatccagacatagttatctgccaatacgtggatgatttgtatgtaggatctgacttagagatagggcaacatagaacaaaagtagaagaactgaggcaacatttgttgaagtggggatttaccacaccagacaacaagcatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccagaa---aaagac---agctggactgttaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttatccagggattaaagtaaggcaattatgtaagctccttaggggagccaaggcactaacagaagtagtgacactaacaaaagaagcagagctagaattggcagaaaacagggagatcctaaaagaaccagtacatggggtgtattatgacccatcaaaagacttaatagcagaaatacagaagcaggatgaaagccaatggacatatcaaatttatcaagagcaatttaaaaatctgaaaacaggaaaatatgcaaaaatg---aggggtgcccacactaatgatgta------agacaattaacagaggcagtgcaaaaaatagccacagaaagcatagtgatatggggaaag---actcctagatttaaactacccatacaaaaagaaacatgggaagcatggtggacagagtattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagtgaaattatggtaccagttagagaaagaacccatagcaggagcagaaactttctatgtagatggagcagctagcagggagactaaattaggaaaagcaggatatgttactaacagaggaagacaaaag---gttgtctccctaactgacacaacaaatcagaagactgagttacaagcaatccagttagctttacaggactcgggatcagaag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+>B.US.03.L8180.FJ469743
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+>B.US.03.PRLS01.FJ469753
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+>B.US.03.PRLS04.FJ469755
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+>B.US.03.PRLS12.FJ469759
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+>B.US.03.PRLS24.FJ469764
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+>B.US.03.SH8233.FJ469770
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+>B.US.04.014837G.FJ469684
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+>B.US.04.268977.KT124758
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+>B.US.04.CR0068P.FJ469695
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+>B.US.04.CR0080N.FJ469697
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+>B.US.04.CR0116Y.FJ469698
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+>B.US.04.CR0345Q.FJ469722
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+>B.US.04.ES10_53.EF363127
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+>B.US.04.ES4_24.EF363124
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+>B.US.04.ES8_43.EF363126
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+>B.US.04.F7165.FJ469732
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+>B.US.04.HIV_US_BID_V5261_2004.JQ403104
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+>B.US.04.L819.FJ469745
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+>B.US.04.SAMI_WGA1.EU547186
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+>B.US.04.SH858.FJ469772
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+>B.US.04.USPI71101EI7y04051pcWG2B9.JN024210
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+>B.US.04.USPI83747EI6y04121pcWG2B5.JN024100
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+>B.US.05.01144G.FJ469682
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+>B.US.05.012286G.FJ469683
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+>B.US.05.04013396_0_flE6.FJ496081
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+>B.US.05.11Pt1302005P1H10.MK383403
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tcttgggagcagca---ggaagcactatgggcgcagcgtca---atgacgctgacggtacaggcc---aga------caa---ttattg---tctggtatagtgcaacagcag---aacaacttg---ctgagagctattgaggcgcaacaacatctgttgcgactcacagtctggggcatcaagcagctccag---gcaagagtcctggctgtggaaagatacttaaaggatcaacagctcctgggaatttggggttgctctggaaaactcatttgcaccactgcagtgccttggaatgct---agt---tgg------------------------------------agtaataaatctctgaatcagatttgg---------gat---aacatgacctggatggag---tgg---gaa-agagaaattgataattacacaggcttaatatacaccttaattgaagaatcgcaa-aaccaacaagaa-aagaatgagcaagaattattggaattagataaatgggcaagtttgtggaattggtttgacataacaaaatggctgtggtatata-aaaatattcataatgatagtaggaggcttggtaggttta-agaatagtttttactgtactttctatagtgaatagagttaggcagggatattcaccattatcg---tttcag---atccgccccccagcc------ccgcgggga------cccgacagg------cccgaaggaatcgaaggagaaggtggagagagagacagagacagatccagtcaattagtggatggattcttagcaattatctgggtcgacctgcggagcctgtgcctcttcagctac---caccgcttgagagacttactcttgattgtagcgaggattctggaa---ctt---ctg---ggacgc---------------------------------------------agggggtgg------gaaaccctcaag---tattgg---------tggaatctcctacagtattggagtcaggaactaaagaatagtgct--gttagcttgctcaacgccacagccatagcagtagctgag-gggacagatagggttatagaagtagtgcaaagagcttggaga------gctgttctccacatacctaca---agaataagacagggcttggaaagggct------ttg-------cta---taa--------------------------------------gatgggtagtaagtggtcaaaa------agtagtgtg---gtt---ggatggcctgctgtaagggaaagaatgagacgagct------------------------------------------------------------gagccagca------------------------------gcagatggggtgggagca---gtatctcgagacctggaaaaacatggagcaatcacaagtagcaatacagcagataccaatgctgat---tgtgcctggctagaagca---------caacaagag---------gga---gaggaggtgggttttccagtcagacctcaggtacccttaagaccaatgacttacaagggagctcta------gatcttagccgctttttaaaagaaaaggggggactg---gaagggttaattcactcccaacaaagacaagatatc---------cttgatctgtgggtctataacaca-caa---ggatacttccctgattggcag---aactacaccccagggccagggatcagatatccactgacctttggatggtgcttcaagctagtaccagttgagccagagaaggtagaagag------gccaatgaagga------gagaacaacagcttgttgcaccctatgagcctgcatgggatgggagatccg---gagaaa---gaagtgttacagtggaagtttgacagccgcctagca-tttcatcacgtagcccgagagatacat---ccggagtac------------------------tacaaggac---taagaactgctgac-------------------------------atcgagctt-------------------------tctacaa----------------------------------------gggactttcc----------------gctg---------------------------------------gggactttcc----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>B.US.05.502_0223_wg1.JF320059
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+>B.US.05.502_1400_FL02.JF320043
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+>B.US.05.502_2008_FL04.JF320484
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+>B.US.05.502_2495_wg02.JF320054
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+>B.US.05.509452.KT124778
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+>B.US.05.CR0175S.FJ469703
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+>B.US.05.CR0208W.FJ469706
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+>B.US.05.CR0312W.FJ469718
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+>B.US.05.L8249.DQ886037
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+>B.US.05.L827.FJ469747
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+>B.US.05.MDR_1c.KF990605
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+>B.US.05.USPI88403EI14y05121pcWG2B7.JN024344
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+>B.US.06.502_0053_wg06.JF320615
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+>B.US.06.502_0062_FL04.JF320613
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+>B.US.06.502_0341_FL05.JF320003
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+>B.US.06.502_0346_wg02.JF320097
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+>B.US.06.502_0572_FL06.JF320038
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+>B.US.06.502_1174_FL09.JF320053
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+>B.US.06.502_1512_FL01.JF320356
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+>B.US.06.502_1619_FL06.JF320126
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+>B.US.06.502_2667_FL03.JF320145
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+>B.US.06.689801.KT124791
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+>B.US.06.CH106_TF1.JN944897
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+>B.US.06.CH148.PL.191206.BE.3.KY112061
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+>B.US.06.CH77E_flA1.FJ496000
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+>B.US.06.CR0047U.FJ469691
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+>B.US.06.CR0078.FJ469696
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+>B.US.06.CR0131.FJ469700
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+>B.US.06.CR0222X.FJ469709
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+>B.US.06.CR0228Q.FJ469710
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+>B.US.06.CR0361T.FJ469723
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+>B.US.06.HIV_US_BID_V3047_2006.JQ403068
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+>B.US.06.HIV_US_BID_V4503_2006.JQ403095
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+>B.US.06.MDR_5a.KF990608
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+>B.US.07.102GW07P5E11.MK383385
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+>B.US.07.502_0364_wg2.JF320563
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+>B.US.07.502_0823_05.JF320530
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+>B.US.07.502_1709_04.JF320467
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+>B.US.07.CR0027M.FJ469689
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+>B.US.07.CR0214.FJ469707
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+>B.US.07.CR0275.FJ469713
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+>B.US.07.CR0295S.FJ469716
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+>B.US.07.CR0339X.FJ469721
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+>B.US.07.HIV_US_BID_V3020_2007.JQ403059
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+>B.US.07.HIV_US_BID_V3021_2007.JQ403060
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+>B.US.07.HIV_US_BID_V3036_2007.JQ403064
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+>B.US.07.HIV_US_BID_V3044_2007.JQ403066
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+>B.US.07.HIV_US_BID_V3053_2007.JQ403071
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+>B.US.07.HIV_US_BID_V3120_2007.JQ403078
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+>B.US.07.HIV_US_BID_V3512_2007.JQ403092
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+>B.US.07.HIV_US_BID_V3515_2007.JQ403093
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+>B.US.07.HIV_US_BID_V4516_2007.JQ403096
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+>B.US.08.116JL08P8F12.MK383397
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+>B.US.08.293050.KT124761
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+>B.US.08.CH302.PL.041608.UT.7.KY112135
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+>B.US.08.CH378.PL.080508.UT.15.KY112149
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+>B.US.08.HIV_US_BID_V3027_2008.JQ403062
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+>B.US.08.HIV_US_BID_V3046_2008.JQ403067
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+>B.US.08.HIV_US_BID_V3048_2008.JQ403069
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+>B.US.08.HIV_US_BID_V3050_2008.JQ403070
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+>B.US.08.HIV_US_BID_V3114_2007.JQ403074
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+>B.US.08.HIV_US_BID_V4120_2008.JQ403031
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+>B.US.08.HIV_US_BID_V4124_2008.JQ403035
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+>B.US.08.HIV_US_BID_V4388_2008.JQ403083
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+>B.US.08.HIV_US_BID_V4391_2008.JQ403086
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+>B.US.08.HIV_US_BID_V4392_2008.JQ403087
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+>B.US.08.HIV_US_BID_V4393_2008.JQ403088
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+>B.US.08.HIV_US_BID_V4394_2008.JQ403089
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+>B.US.08.HIV_US_BID_V4397_2008.JQ403091
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+>B.US.09.C1P.GU733713
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+>B.US.09.DEMB09US002.JX140657
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+>B.US.09.DEMB09US003.KC473824
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+>B.US.10.100sgor2010P5E9.MK383384
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+>B.US.10.10CB4_45E6.KF526141
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+>B.US.10.505_0695a.WG06.MG196787
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+>B.US.10.505_1962a.WG03.MG197136
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+>B.US.10.505_2483a.WG03.MG197210
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+>B.US.10.DEMB10US001.KC473825
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+>B.US.10.DEMB10US003.KC473826
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+>B.US.10.DEMB10US004.KC473827
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+>B.US.10.DEMB10US007.KC473828
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+>B.US.10.DEMB10US009.KC473829
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+>B.US.10.Pt1_DNA_2.KU677990
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+>B.US.10.Pt4_DNA_5.KU678074
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+>B.US.11.20CB4_46F1.KF526265
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+>B.US.11.22CC9_induced.KF526312
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gaaaaccagagaa--------gctctctcgacgca-ggactcggcttgct---gaagcgcgcacggcaagaggc-------------gagg-gg--cggc-----gactggtgagtacgcc-------------------------atatttttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcggtatttagcgggggagaattagataagtgggagaaaattcggtta---agg------cca---gggggaaagaaaaaatataagttaaaacatatagtatgggcaagcagggaactagaaagattcgccgtcaaccctggcctgttagaaacatcagacggctgtagacaaatactgggacagttacaaccagcc---cttcagacaggatcggaagaacttagatcattatataatacagta---gcaaccatctattgtgtgcatcaaaggatagatgtaaaagacaccaaggaagccttagacaagatagaggaagagcaaaacaaaagtaag------------------------aaaaaggcacagcaagcagcagct---------------------gacacagga---------------gacaaaaacaacagccag------------------------gtcagccaaaattaccctata------------gtgcagaacctacaggggcaaatggtacatcaggccctatcacctagaactttaaatgcatgggtaaaagtagtagaagagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaataccatgctaaacacagtggggggacatcaa---gcagcaatgcaaatg---ttaaaagag---actatcaatgaagaagctgcagagtgggatagattgcat---cccgtgcaggca---gggcctgttgcaccaggccagcta---agagaaccaaggggaagcgatatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------catactcca---cct---atc---ccagta---ggagaaatctataaaagatggataatcatgggattaaataagatagtaaggatgtatagccctaccagcattctggacataaaacaaggaccaaaggaaccctttagagactatgtagaccggttctataaaattctgagagccgagcaagcttcacatgatgtaaaaaagtggatgacagaaaccttgttggtccagaatgcgaacccagattgtaagaccattttaaaagcattaggaccagcagctacactagaagaaatgatgacagcatgtcagggagtgggaggacctggtcataaa---gcaagagtgttggctgaa------gcaatg---agtcaactaaacaat---------------------tcaactaccata---atgatg------cagagagacaat---------ttt---aggaaacaaagaaag------attgttaaatgcttcaattgtggcaaagaaggg---cacatagccaaaaattgcagggcccctaggagaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagattgt------------------gaaagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---gag---gccaggaaactttcttcagagcagaccagagccaacagc---------------cccaccagaagttcagagcaggctagagccaacagccccacctcaaga------agagagcttcaggtt------------tgggggggagacaacaac---tccctc------------------------------tcagaa---------------gcaggagac------------gatagacaa---------------------------aga------------gatgta------tcctttaacctccctcaaatcactctttggcaacgacccctcgtcacaataaagataggggggcaactaaaggaagctctattagatacaggagcagatgatacagtagta---gaagaa---atgagtttatcaggaaggtggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacaatat---gaacagatacccatagaaatttgtggacataaagctataggtacagtattagtgggacctacacctgtcaac---ataattggaagaaatctgttgactcagattggttgcactttaaattttcccattagtcccattgaaactgtaccagtaaaattgaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaagcattagtagaaatttgtaca------gaaatggaaaaggaagggaaaatttcaaaa---attgggcct---gaaaatccatacaatactccagtatttgccataaagaagaaagacagt------actaaatggaggaaattagtggatttcagagaacttaataagagaactcaagacttctgggag---gttcaa------tta---gggata---------------------------ccacatcccgcagggttaaaaaagaaa---aaa------tcagtaacagtattggatgtgggtgatgcatac---ttttcagttcccttagataaagaattcaggaagtatactgcattcaccatacctagtataaacaatgagacaccagggattagatatcagtacaatgtgctgccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatcttagagccttttagagaacaaaataaagacatagttatctatcaatacatggacgatttgtatgtaggatctgacttagaaatagggcagcatagaacaaaaatagaggaactgagacaacatctgttgaggtggggattaaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacaacctatagagctgccagat---aaaaac---agctggactgtcaatgacatacaaaagttagtgggaaaattaaattgggcaagtcagatatacccagggattaaagtaaagcaattatgtaaactccttaagggaaccaaaacgttaacagaagtaataccactaacagaagaagcagagctagaactagcagaaaacagggagattttaaaagaaccagtacatggagtgtattatgacccaacaaaagacttaatagcagaattacagaagcaggggcaaggccaatggacatatcaaatttaccaagagccatttaaaaatctgaaaacaggaaaatatgcaagagtg---aggggcgcccacactaatgatgta------aaacaattaacagaggcagtgcaaaaaatagccacagaaggcatagtgatatggggaaag---actcctaaatttaaactacccatacaaaaggagacatgggaaacatggtggacagagtattggcaagctacctggattcctgagtgggagtttgtcaatacccctcccttagtaaaattatggtaccagttagagaaagaacccatattaggagcagaaactttctatgtagatggggcagccaatagggaaagtaaatcaggaaaagcaggatatgttacagacaggggaagacagaag---gtcatctccctaactgacacaacaaatcagaagactgaattacaagcaattcatctagccttgcaggattcgggaatagaag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tcttgggagcagca---ggaagcactatgggcgcagcgtca---gtaacgctgacggtacaggcc---aga------cta---ttgctg---tctggtatagtgcaacagcag---aacaatctg---ctgagggctattgaggcgcaacagcatctgttgcaactcacagtctggggcatcaagcagctccag---gcaagagtcctggctgtggaaagatacctaagggatcaacagctcctggggatttggggttgctctggaaaactcatttgcaccactaatgtaccttggaatgct---agt---tgg------------------------------------agtaataaaactatgaatgacatctgg---------gat---aacatgacctggatgcag---tgg---gag-agagaaattgacaattacacagacttaatatacgccttacttgaagaatcgcag-aaccaacaagaa-aagaatgaacaagaattattggcattagataaatgggcaagtttgtggaattggtttgatataacaaaatggctgtggtatata-aagatattcataatgatagtaggaggcctggtaggttta-agaatagttttcactgtactttctatagtaaatagagttaggcagggatactcaccattgtcg---tttcag---acccactccccagcc------ccgagggga------cccgacagg------cccggaggaatcgaagaagacggtggagaaagaaacagagatacatccggcttcttagtgaatgggttcttggctatcatctgggtcgacctgcggagcctgtgcctcttcatttac---caccgcttgagagacttactcttgattgtcgcgaggattgtggaa---ctt---ctg---ggacag---------------------------------------------agggggagg------gaagtcctcaaa---tattgg---------tggaatctcctgcagtattggggtcaggagctaaagaatagtgct--gttagcttgtttaacgccacagcaatagcaatagctgag-gggacagatagggttatagaaatagtgcaaatagcttttaga------gctattctccacatacctcgg---agaataagacagggctttgaaagggct------ttg-------cta---taa--------------------------------------gatgggtggcaagtggtcaaaa------cgtagtggg---ggt---ggatggaatgctgtaagggaaagaatgagacgaactaggccagcagat------------------------------------------------gagccagca------------------------------gcagctggggtgggagca---gcatctcgagacctggaaagacatggagcactcacaagtagcaatacaccaactaacaatgctgct---tgtgcctggctagaagca---------caacaagag---------gat---gaggacgtgggttttccagtcagacctcaggtacctttaagaccaatgacttacaagggagcctta------gatcttagccactttttaaaagaaaaggggggactg---gaagggctaatttactcccaaaaaagacaagatatc---------cttgatctgtgggtctataacacg-caa---ggctacttccctgactggcag---aactacacaccagggccagggatcagatacccactgtgttttgggtggtgcttcaaactagtgccagtctcgccagagaagatagaagag------gccaatgaagga------gagaacaactccttgttacaccccatgagccagcatggaatggatgacccg---gagaga---gaggtgttagtgtggaagtttgacagccgcctggcg-tttcatcacgtggcccgagagatacat---ccggagtac------------------------tacaaggactgctgac-----------------------------------------tttgagctt-------------------------tctacaa----------------------------------------gggactttcc----------------gctg---------------------------------------gggactttcc----------------------------------------------------------------------------------gggaggc------------gtggcc-tgggcgggacc-----------gggg-agtg-gc-gagccc--tcag-a-----tgctgcat--ataagcag-c-cgcttttc-gc-c-tg-ta--ctgg-g----tc-tctc-tg--------g-ttag----a--ccagat---------------------------------------------------------------------cagag---------------cc-tggg-agctc--------tctgg-----------c------taac-t-agggaac-ccactgctt--aa-gcct----c-aat--aaagc-ttgc---c-----------tt--ga--g-tgct-tcaag-tagtgtgtgcc-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>B.US.11.23CB6_induced.KF526323
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------taaaaccagagaa--------gttctctcgacgca-ggactcggcttgct---gaagcgcgcacagcaagaggc-------------gagg-gg--cggc-----gactggtgagtacgcc-----------------------atttatttttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggagaattagataaatgggaaagaattcggtta---cgg------cca---ggaggaaagaaaaaatatcaattaaaacatatagtatgggcaagcagggagttagaacgatttgcagttaatcctggccttttagagacatcagaaggctgcagacagatactgagacagctacaaccatcc---cttcagacaggatcagaggaacttagatcattatataatacagta---gcaaccctctattgtgtgcatcaaaagatagaggtaaaagacaccaaggaagccttagataaggtagaggaagagcaaaacaattgtaagaaaaaggcacagcaagcggcagctgctgcagga---------aacagcagccaagct------------gacacagga------------------aac---agcaggcaa------------------------gtcagccaaaattaccctata------------gtgcagaacctacaggggcaaatggtacatcagcccatagcacctagaactttaaatgcatgggtaaaagtagtagaagagaag------gcctttagcccagaagtaatacccatgttttcagcattagcagaaggagccaccccacaagatttaaacctcatgctaaacgcagtggggggacatcaa---gcagctatgcaaatg---ttaaaagag---accatcaatgaggaagctgcagaatgggatagagtgcat---ccagcgcaggca---gggcctgtcgcaccaggccagata---agagacccaaggggaagtgacatagcaggaaccactagtaac---cttcaggaacaaataacatggatgaca---------aataatcca---ccc---atc---ccagta---ggagaaatctataagagatggataatcctgggattaaataaaatagtaagaatgtatagccccaccagcattctggacataagacaaggaccaaaagaaccctttagagactatgtagatcggttctataaaactctaagagccgagcaagcttcacaggatgtaaaaaattggatgacagaaaccttgttggtccagaatgcgaacccagattgtaaaactattttaaaagcattagggccaggagctaccctagaagaaatgatgacagcatgccaaggagtagggggacctagccataag---gcaagagtcttggctgaa------gcaatg---agccaagtaacaaat---------------------tcaactgccata---atgatg------cagaaaggcaat---------ttt---aggaatcaaagaaaa------actgttaagtgtttcaattgtggcaaagaagga---cacatagccaaaaattgcagggcacctagaaaaaaggggtgttggaaatgtggaagggaaggacaccaaatgaaagattgc---------------actgagagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---aag---gccagggaatttccttcagaacagaacagagccaacagc------------------------------------------------------cccaccaga------agagatcttcaggtt------------tggggaggagac---aac---tcactc------------------------------tcagaa---------------gaaggaaca------------gttagacaa---------------------------gga------------actgta------tcctttagcctccctcaaatcactctttggcaacgacccctcgtcacaataaagataggggggcagctaaaggaagctctattagatacaggagcagatgatacagtatta---gaagaa---atgaatttgccagggaaatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcaaatacccatagaaatctgtggatataaaactgaaggtacagtattaataggacccacacctgtcaac---ataattggaagaaatctgttgactcagcttggttgcactttaaattttcctattagtcctattgaaactgtaccagtaaaactaaaaccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaagcattggtaaaaatttgtaca------gaaatggaaaaagaaggaaaaatttcaaaa---attgggcct---gaaaatccatataatactccagtatttgccataaagaaaaaggatagt------actaaatggagaaaattggtagatttcagagaacttaataaaagaactcaagacttttgggaa---gttcaa------tta---ggaata---------------------------ccacatcctgcagggttaaaaaagaaa---aaa------tcagtaacagtattggatgtgggagatgcatat---ttttcagttcctctagataaagagttcaggaagtatactgcctttactatacctagtataaacaatgagacaccaggaattagatatcagtacaatgtgcttccacagggatggaaaggatcgccagcaatattccagagtagcatgacaaaaatcttagaaccttttagacaacaaaatccagaaatagttatctaccaatacatggatgatttgtatgtaggatctgatttagaaatagggcagcacagaacaaaaatagaggaattaagagaacatctattaaagtggggatttaccacaccagacaaaaaacatcagaaagaacctccatttctttggatgggttatgaactccatcctgataaatggacagtacagccaatagcattgccagaa---aaggac---agctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttatccagggattagagtaaagaatttatgtaaactccttagagggacaaaagcattaacagaagtagtaccactaacagaagaagcagagctagaactagcagaaaacagggagattctaaaagaaccagtacatggagtgtattatgacccatcaaaagaattaatagcagaaatacagaagcagggatacggccaatggacatatcaaatatatcaagagccatttaaaaatctgaaaacaggaaagcatgcaagaacg---aggggtgcccacactaatgatgta------aaacaattaacagaggcagtgcaaaaaatagccatggaaagcatagtaatatggggaaag---actcctaaatttaaactacccatacaaaaagaaacatgggaaacatggtggacagagtattggcaggccacctggatccccgagtgggagtttgtcaatacccctcccctagtaaaattatggtaccagttagagaaagaacccatagtaggagcagaaactttctatgtagatggggcagctaatagggaaactaaattaggaaaagcaggatatgttactgacaaaggaagacaaaag---gttgtccccctaacggacacaacaaatcaaaaaactgagttacatgcaatttatctagctttgcaggattcagggtcagaag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+>B.US.11.361974.KT124766
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+>B.US.11.481811.KT124775
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+>B.US.11.505_1982a.WG07.MG197146
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+>B.US.11.950965.KT124809
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+>B.US.11.AMBI_CLONE.KU641402
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+>B.US.11.CP13_2.KF384800
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tcttgggagcagca---ggaagcactatgggcgcagcggca---gtgacgctgacggtacaggcc---aga------cta---ttattg---tctggtatagtgcaacagcaa---aacaacttg---ctgagagctattgaggcgcaacagcatatgttgcaactcacagtctggggcattaagcagctccag---gcaagagtcctggctctggaaagatacctaagggatcaacagctcctgggaatttggggttgctctggaaaactcatttgcaccactactgtgccttggaatgct---agt---tgg------------------------------------agtaatagatctctagatgagatttgg---------gat---aacatgacctggatgaaa---tgg---gaa-agagaaattgacaattacacaggcttaatatacaacttacttgaacaatcgcag-aaccagcaagaa-aagaatgaacaagaattgttggaattggatcaatgggcaagtttgtggaattggttccacataacaaattggctgtggtatata-aaaatattcataatgatagtaggaggcttggtaggctta-agaatagtttttgctatactttctgtagtgaatagagttaggcagggatactcacctttatcg---tttcag---acccacttcccagcc------ccgcgggga------cccgacagg------cccgaaggaatcgaagaaggaggtggagagggagacaacgacagatccaggcgatcagtggatggcttcttagcaattgtctgggtcgacctacggagcctgtgcctcttcagctac---caccgattgagagacttactcttgattacagcgaggggtctggaa---ctt---ctg---gggcgc---------------------------------------------ggggtgtgg------ggagtcctcaaa---tactgg---------tggaatctcctccagtattggagtcaggagataaagaatagtgct--gttagcttgctcaacgccacagctatagcagtagctgag-tggacagatagggttatagaagtattacaaagagctggtaga------gctattatccacatacctaca---agaataagacagggcttggaaagggct------ttg-------caa---taa--------------------------------------gatgggtggcaagtggtcaaaa------aatagaata---gct---ggatggggtgctataagggaaaaaatgagaaaagctgagccagcagca------------------------------------------------gagccagca------------------------------gcagaaggggtaggagca---gcatctcgagacctggaaaaatatggagcaatcacaagtagcaatacagcagctaccaatgctgat---tgtgcctggctagaagca---------caagaggag---------gag------gaagtgggctttccagtcagacctcaggtaccgttaagaccaatgacttacaagggagctgta------gatattagccactttttaaaagaaaaggggggactg---gaagggctaatttacagccaaagaagacaagatatc---------cttgatctatggatctaccacaca-cag---ggctatttccctgattggcag---aactacaccccagggccagggatcagatatccactgacctttggatggtgcttcaagctagtaccagttgacccagagaaggtagaagag------gccaatgaagga------gagaataacagcttgttacaccctatgagccaacatgggatagatgaccca---gagaaa---gaagtgctaatgtggaagtttgacagccacctagcg-tttcgtcacatggccaaagagctgcat---ccggagtac------------------------tacaagaactgctgac-----------------------------------------atcgagctc-------------------------tttacaa----------------------------------------gggactttcc----------------gc-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>B.US.11.CP4_2B.KF384802
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+>B.US.11.CP5_3A.KF384803
+------------------------------------------------------------------------------------------------------------------------------------atggtgcttcaagctagtaccagttgagcca------gcagccaat--gcc---aatgaaggagagaacgacagcctgttacaccctataagccagcatgggatggaggactcggagagagaagtgttagtgtggaagtttgacagccgcctagcattt---catcacgtagcccgagagctg------cat--ccggagtat---------------------------tacaagaactgatgacatcgagctttctacactgctga---------catcgagcttt------------ctacaa-----gggactttcc-------------------gct--ggggactttcc--aggg-aggcgtgga--------------ctggg-cgggact-gggg-agtggc-gag-ccctcaga-tgctgcatataagcag-ctgctttttgcctgtact-g-ggtctctc--tggttagaccagatc-t-gagcctgggagctctctgg-ctaac-taggg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-ttc--aa-g-----ta-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------gctagagatc-------cctcagaccctt-ttag-t-cagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------agaaaccagagga--------gctctctcgacgca-ggactcggcttgct---gaagtgcgcacggcaagaggc-------------gagg-gg--cggc-----gactggtgagtacgcc-------------------------aaatttttgact----------agcgga-gg---------ctaga-----------a--g--------------gc-c-a-g--ac--------------------------atggggtcgagagcgtcagtattaagcgggggagaattagacaaaggggaaaaaattcggtta---agg------cca---gggggaaagaaaaaatatcaattaaaacatatagtatgggcaagcagggagctagaacgattcgccgttaatcctggcctgttagaaacatcagaaggctgtaggcaaatactgggacagttacaaccgtcc---cttcagacaggatcagaagaacttagatcgctatataatacagta---gcaaccctctattgtgtgcatcaaaagatagaggtaaaagacaccaaggaagctttagataagatagaggaagagcaaaacaaaagtaag------------------------aaaaaagcacagcaagcagcagct---------------------gacacagga------------------aac---agcagcaag------------------------gtcagccaaaattatcctata------------gtgcagaacctccaggggcaaatggtacaccagcccatatcacctagaactttaaatgcctgggtaaaagtagtagaagagaag------gctttcagcccagaagtaatacccatgttttcagcattagcagaaggagccaccccacaagatttaaacaccatgctaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagag---accatcaatgaggaagctgcagaatgggatagattgcat---ccagtgcatgca---gggcctattgcaccaggccagatg---agagaaccaaggggaagtgacatagcaggaactactagtaac---cttcaggaacaaataggatggatgaca---------cataatcca---cct---atc---ccagta---ggagaaatctataaaagatggataatcctaggattaaataaaatagtaaggatgtatagtcctaccagcatcttggacataagacaaggaccaaaagaaccctttagagactatgtagaccggttctataaaactctaagagccgagcaagcttcacaagaggtaaaaaattggatgacagaaaccttgttggtccaaaatgcaaacccagattgtaagaccattttgaaagcattgggaccagcagctacactagaagaaatgatgacagcatgtcagggagtgggaggacctggccataaa---gcaagagttttagcggaa------gcaatg---agccaagtaacaaat---------------------tcagctaccata---atgaca------cagagaggcaat---------ttc---aggaaccaaagaaag------attgttaagtgtttcaattgtggcaaagaaggg---cacatagccagaaattgcagggccccgaggaaaaggggctgttggaaatgtggaaaagaaggacaccaaatgaaagattgt---------------actgagagacaggctaattttttagggaagatctggcc---ttcccacaa------ggg---gag---gccagggaactttcttcagagcagaccagagccaacagc------------------------------------------------------cccacccga------agagagtttcaggtt------------tggggaagagacaacaac---tccctc------------------------------tcagaa---------------gcaggagct------------gatagacaa---------------------------gga------------acagta------tcctttagcttccctcagatcactctttggcaacgacccctcgtcacaataaagataggggggcaaataaaggaagctctattagatacaggagcagatgatacagtatta---gaagaa---atgaatttgccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcaaatactcatagaaatctgtggacataaagctatgggtacagtattagtaggacctacacctgtcaac---ataattggaagaaatctgttgactcagattggttgcactttaaatttccccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaaattaaacaa---tggccattgacagaagaa---aaaataaaagcattaatagaaatttgtaca------gaaatggaaaaggaaggaaaaatttcaaaa---attgggcct---gaaaatccatataatactccagtatttgcaataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagagaactgaataagaaaactcaagacttctgggaa---gttcaa------tta---ggaata---------------------------ccacatcccgcagggttaaaaaagaaa---aaa------tcagtaacagtactagatgtgggtgatgcatat---ttctcagttcccttagataaagacttcaggaagtatactgcatttaccatacctagtataaacaatgagacaccagggattagatatcagtataatgtgcttccacaaggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaattttagagccttttagaaaccaaaatccagaaatagttatctatcaatacatggatgacttgtatgtaggatctgatttagaaatagggcagcatagaacaaaaatagaggaactgagacaacatctgttgaaatgggggtttaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaacttcatcctgataaatggacagtacagcctatagagctgccagaa---aaggac---agctggactgtcaatgatatacagaagttggtgggaaaattgaattgggcaagtcagatttatgcagggattaaagtaaagcaattatgtaaactccttaggggagccaaggcactaacagaagtagtaccactaacagaagaagcagagctagaactggcagaaaacagggaaattctaaaggaaccagtacatggagtgtactatgacccatcaaaagacttaatagcggaaatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagctatataaaaatctgaagacaggaaaatatgcaagaatg---aggggtgcccacactaatgatgta------aagcaattaacagaggtagtgcaaaaaatagccacagaaagcatagtaatatggggaaag---actcctaaatttagactaccaatacaaaaggaaacatggggagcatggtggacagagtattggcaggccacctggattcctgagtgggagtttgtcaatacccctcccttagtgaaattatggtaccagttagagaaagaacccatagtaggagcagaaaccttctatgtagatggggcagctaacagggagactaaagtaggaaaagcaggatatgttactaacagaggaagacaaaaa---gttgtctccctaacagacacaacaaatcagaagactgagttacaagcaattcatctagctttgcaggattcaggattagaag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+>B.US.11.CP6_2E.KF384804
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tcttgggagcagca---ggaagcactatgggcgcagcgtca---atgatgctgacggtacaggcc---aga------caa---ttattg---tctggtatagtgcaacagcag---aacaatctg---ctgagggctattgaggcgcaacaacatctgttgcaactcacagtctggggcatcaagcagctccag---gcaagagtcctggctgtagaaagatacctaaaggatcaacagctcctgggaatttggggttgctctggaaaactcatctgcaccactaatgtgccttggaacact---agc---tgg------------------------------------agtaataaatctctaaaacagatttgg---------gac---aacatgacctggatggag---tgg---gaa-agagaaattgacaactacacaagtgtaatatacaccttaattgaacaatcgcaa-aaccagcaagaa-aagaatgaagaagagttattatctttagataaatgggacaatttatggaattggtttaacataacaaactggctgtggtatata-aaaatattcataatgatagtaggaggcttgataggttta-agaatagtttttactgtactttctatagtaaatagagttaggcagggatattcaccattatcg---ttccag---acccacctcccaacc------ccgagggga------cccgacagg------cccgacggaatcgaagaagaaggtggagagagagacagagacagatccggtcaatcagtgaatggattcttagcaatcatctgggtcgacctgcggagcctgttcctcttcagctac---caccgcttgagagacttactcttgattgtaacgaggattgtggaa---ctt---ctg---ggacgc---------------------------------------------agggggtgg------gaagccctcaaa---tattgg---------tggaatctcctccagtattggagtcaggaactaaagaatagtgct--gtaagcttgctcaatttcatagctatagcagtagctgag-gggacagataggatcatagaagtattacaaagaattggtaga------ggcatcctccacatacctaca---agaataagacagggcttagaaaggctt------ttg-------cta---taa--------------------------------------aatgggtggtaagtggtcaaaa------agtagtgtg---att---ggatggcctgctataagggaaagaatgagacgagct------------------------------------------------------------gagccagca------------------------------gcagagggggtgggagca---gcatctcgagacctggaaaaacatggggcaatcacaagtagcaatacaccagctaccaacgccgat---tgtgcctggctagaagca---------caacaagaa---------gag---gaggaagtgggttttccagtcagacctcaggtacctttaagaccaatgacttacaatgcagctcga------gaccttagcttctttttaaaagaaaaggggggactg---gaagggctaatttactcccaaagaaggcaagatatc---------cttgatctgtggatctataacaca-caa---ggctacttccctgattggcag---aactacacaccagggccagggatcagatatccactgacctttggatggtgcttcaaactagtaccagttgagccagataaggtagaagag------gccaatgaagga------gagaataacagcctgttacaccctatgagcctgcatgggatggatgacccg---gagaaa---gaagtgctagaatggaggtttgacagccgcctagca-tatcatcacatggcccgagagctgcat---ccggagtac------------------------tacaagaactgctga--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>B.US.11.DEMB11US002.KC473831
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------agtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------agaaaccagagga--------gctctctcgacgca-ggactcggcttgct---gaagcgcgcacggcaagaggc-------------gagg-gg--cggc-----gaacggtgagtacgcc------------------------aaaacttttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggaggattggatcgatgggaaaaaattcggtta---agg------cca---ggaggaaagaaacaatataaattaaaacatatagtatgggcaagcagggagctagaacgattcgcagtcaatcctggtctgctagaaacaccagaaggctgcagacaaataatgggacagctacaaccagcc---cttcagacaggatcagaagaacttaaatcactatataatacagta---gcagtcctctattgtgtacatcaaaggatagacgtaagagacaccaaggaagctctagataagatagaggaagagcaaaacaaatgcaag------------------------aaaaaggcacaacaagcagcagct---------------------gacacagga------------------aac---aacagtcag------------------------gtcagccaaaattaccctata------------gtgcagaatctccaggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgggtaaaagtagtagaagagaag------gctttcagcccagaagtaatacccatgttttcagcattatcagaaggagccaccccacaagatttaaacaccatgctaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagag---accattaatgaggaggctgcagaatgggatagattacat---ccagtgcatgca---gggcctattgcaccaggccagatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggagcaagtaggatggatgaca---------agtaatcca---cct---atc---ccagta---ggagaaatctataaaagatggataatcatgggattaaataaaatagtaaggatgtatagccctactagcattttggacataagacaaggaccaaaagaacccttcagagactatgtagaccggttctataaaactctaagagccgagcaagcttcacaggaggtaaaaagttggatgacagaaaccttgttggtccaaaatgcaaacccagattgtaagaccatcttaaaagcattgggaccagcagctacactagaagaaatgatgacagcatgtcagggagtgggaggacccagccataaa---gcaagagttttggctgaa------gcaatg---agccaagtaacaaat---------------------ccagctaacata---atgatg------cagaggggcaat---------ttt---aggaaccaaagaaaa------attgttaagtgtttcaattgtggaaaagaaggg---catatagccagaaattgcaaggcccccaggaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagattgc---------------actgagagacaggctaattttttagggaaaatctggcc---ttccaacaa------ggg---gag---gccaggaaactttcttcagtgcagaccagagccaacagc------------------------------------------------------cccaccaga------ggagagcttcaggtt------------tggggaggagacaacagg---tccctc------------------------------tcagaa---------------gcaggagcc------------gatagacaa---------------------------gga------------acggta------tcctttagcttccctcaaatcactctttggcaacgacccctagtcacagtaaagatagggggacaactaaaggaagctttattagatacaggagcagataatacagtatta---gaagaa---atgaatttgccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacaatat---gatcagatacccatagaaatttgtggacatagagccataggtacagtgttaataggacctacacctgtcaac---ataattggaagagatctgttgactcagattggttgcactttaaattttcccattagtcctattgacactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaagcattagtagaaatttgtaca------gaaatggaaaaggaaggaaaaatttcaaag---attgggcct---gaaaatccatacaatactccaatatttgccataaagaaaaaggacagt------actaaatggagaaaattagtagatttcagggaacttaataagaaaactcaagacttctgggaa---gtgcag------tta---ggaata---------------------------ccacatcccgcagggctaaaaaagaaa---aaa------tcagtaacagtactggatgtgggtgatgcatat---ttttcagttcccttagatccagacttcaggaagtatactgcatttaccattcctagtataaacaatgagacaccaggaattagataccagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaagaatcttggagccttttagaaaacagaatccagaattagttatctatcaatacatggatgatttgtatgtaggatctgacttagaaatagggcagcatagaacaaaaatagaagaactgagagaacatctattgaagtgggggtttaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagaactgccagag---aaggac---agctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcaaatttacccagggattaaggtaagacaattatgtaaactccttaggggaaccaaagcactaacagaagtagtaccactaacagcagaagcagagctagaactggcagaaaacagggagattctaaaagaaccagtacatggggtgtattatgacccatcaaaagacttaatagcagaaatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaaaattctgaaaacaggaaggtatgcaagaatg---aggggtacccacactaatgatgta------aagcaattaacagaggcagtgcaaaaaatagccacagaaagtatagtaatatggggaaag---acccctaaatttaaactgcccatacagaaagaaacatgggaagcatggtggacagagtattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagttaaattatggtaccagttagagaaagaacctataatgggggcagaaaccttctatgtagatggagcagctaacagagaaactaaattaggaaaagcaggatatgttactaacagaggaagacaaaag---gttgtctccctaactgacacaacaaatcagaagactgagttacaagcaattcatctagctttgcaggattcaggatcagaag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+>B.US.11.DEMB11US006.KC473833
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+>B.US.11.DEMB11US015.KC473835
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+>B.US.11.ES22_27.KF384808
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+>B.US.11.ES39_42.KF384810
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+>B.US.11.ES40_24.KF384811
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+>B.US.11.VC3_14.KF384812
+------------------------------------------------------------------------ttccctgattggcagaactacacaggagggccaggg-atcagatatccactgacctttggatggtgcttcaagctagtaccagttgagccagaccaggtggaaaag--gag---aatgaaggagagaacaaatgcttactgcaccctatgagccagcatgggatggatgaccctgagaaagaagtgttaatatggaagtttgacagccgcctagcgttc---catcacatggcccgagaactg------cat--ccggagtac------------------------tacaaagactgctgacatcgagctttctacctgctga-------------catcgagcttt------------ctac---aa--gggactttcc-------------------gct--ggggactttcca-agga-aggtgtggc--------------ctggg-cgggact-gggg-agtggc-gag-ccctcaga-tgctgcatataagcag-ctgctttctgcctgtact-g-ggtctctc--tagctggaccagatc-t-gagcctgggagctctctgg-ctagc-taggg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-ct-gagtgc-ttc--aa-g-----ta-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------tctagagatc-------cctcagac--tc-ctag-tcagtgtggaaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------gaaaaccagagga--------gctctctcgacgca-ggactcggcttgct---gaagcgcgctcggcaagaggc-------------gagg-gg--cggc-----gactggtgagtacgcc------------------------aaaaactttgact----------agcaga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagtgggggagaattagatagatgggaaaaaattcggtta---agg------cca---gggggaaagaaacaatatagactaaaacatatagtatgggcaagcagggaactagaacgattcgcagttaaccccagcctgttagaaacatcagaaggctgtagaaaaatattggaacagctacaaccatcc---cttcagacaggatcagaagaacttagatcattatataatacagta---gcaaccctctattgtgtacatcaaaggatagatataaaagacaccaaggaagctttagataaaatagaggaagagcaaaacaaaagtaag------------------------aaaatggcacagcaagcagcagct---------------------gacaaagga------------------aac---agtaaccag------------------------gtcagccagaattaccctata------------gtgcagaacctccaggggcaaatggtacatcaggcactatcacctagaactttaaatgcatgggtaaaagtagtagaagagaag------gctttcagcccagaagtaatacccatgttttcagcattatcagaaggagccaccccagcagatttaaacaccatgctaaacacaatagggggacatcaa---gcagccatgcagatg---ctaaaagag---accatcaatgaggaagctgcagaatgggatagattgcat---ccagtgcatgca---gggcctatagcaccaggccagatg---agagaaccaaggggaagtgacatagcaggaactactagtaac---cttcaggaacaaataggatggatgaca---------aataatcca---cct---atc---ccagta---ggagaaatctataaaagatggataatcctgggactaaataaaatagtaaggatgtatagtcctaccagcattctggacataaagcaaggaccaaaggaaccctttagagactatgtagaccggttctataaaactctaagagccgagcaagcgtcacaggaggtaaaaaattggatgacagaaaccttgttggtccaaaatgcgaacccagattgtaagactattttaaaagcattaggaccaggagccacactagaagaaatgatgacagcatgtcagggagtgggaggacccagccataaa---gcaagagttttggctgaa------gcaatg---agccaagtaacaaat---------------------tcagccactgta---atgatg------cagagaggcaat---------ttt---aagaaccaaaaaagg------actgttaaatgcttcaattgtggcaaagaaggg---cacatagccagaaactgcagggctcctaggaagaagggctgttggaaatgtggaagggaaggacaccaaatgaaagattgt---------------actgagaggcaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagagcagaccagagagcagaccagagccaacagc------------------------------------------cccaccaga------agagagcttcaggtt------------tggggaagagacagcaac---tccctc------------------------------tcagaa---------------gcaggagcc------------gacagacaa---------------------------gga------------actgta------tcccttagcttccctcaaatcactctttggcaacgacccctcgtcacaataaaaatagggggggaactaaaggaagctctattagatacaggagcagatgatacagtatta---gaagaa---atgaatttgccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcagataaccatagaaatatgtggacataaagctgtaggtacagtattaataggacccacacctgtcaac---ataattggaagaaatctgttgacacagattggttgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagtcaaacaa---tggccattgacagaagaa---aaaataaaagcattagtagaaatttgtaca------gaaatggaaaaggaagggaaaatttcaaaa---attgggcct---gacaatccatacaatactccagtatttgccataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctgggaa---gttcaa------tta---ggaata---------------------------ccacatcccgcagggttaaaaaagaaa---aaa------tcagtaacagtactagatgtgggtgatgcatat---ttctcagttcccttagataaagacttcaggaagtatacagcatttaccatacctagtataaacaatgagacaccagggattagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatcttagagccttttagaaaacaaaatccagacatagttatttatcagtacgtggatgatctgtatgtaggatctgacttagaaatagagcagcatagaacaaaaatagaggaactgagacaacatctgttgaaatggggatttaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctataaagttgccagaa---aaagac---agctggactgtcaatgacatacaaaagttagtgggaaaattgaattgggcaagtcagatttatgcaggaattaaagtaaagcaattatgtagactccttaggggaaccaaatcactaacagaagtagtaccactaacagaagaagcagagctagaactagcagaaaacagggagattctaaaagagccagtacatggagtgtactatgacccatcaaaagacttaatagcagaaatacagaagcaagggcaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatgcaagaacg---aggggtgcccacactaatgatgta------aaacaattgacagaggcagtgcaaaaaatagccacagaaagcatagtaatatggggaaag---gttcctaaatttaaactacccatacaaaaagaaacatgggaaacatggtggacagagtattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagtgaaattatggtaccagttagaaaaagaacccatagtaggagcagaaactttctatgtagatggggcatctaacagggagactaaattaggaaaagcaggatatgttactaacaaaggaagacaaaag---gttgtctccctaactgacacaaccaatcaaaagactgagttacatgcaattcatctagctttgcaggattcaggatcagaag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+>B.US.11.VC5_3.KF384813
+-----------------------------------------------------------------------------tgattggcagaactacacaccagggccaggg-gtcagatatccactgacttatggatggtgcttcaagctagtaccagttgatccagagaaggtagaagag--gcc---aatgaaggagagaataacagcttgttacaccctatgagtctgcatgggatggaggacccggagaaagaagtgttagcctggaggtttgacagccacctagcattc---catcacgtggcccgagagata------cat--ccggagtac------------------------tacaagaactgctga-----------------------------------catggagcttt------------ctac-------gggactttcc-------------------gct--ggggactttcca--ggg-aggcgtgac--------------ctggg-cgggacc-gggg-agtggc-gag-ccctcaga-cactgcatataagcag-ctgctttttgcctgtact-g-ggtctctc--tggttagaccagatc-t-gagcctgggagctctctgg-ctaac-taggg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-ttc--aa-g-----ta-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccctt-ttaa-t-cagagtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------ggaaaccagagga--------gctctctcgacgca-ggactcggcttgct---gaagcgcgcacggcaagaggc-------------gagg-gg--cggc-----gactggtgagtacgcc------------------------aaaaattttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggagaattagatagatgggaaaaaattcggtta---agg------cca---ggaggaaagaaaaagtacaaattaaaacatatagtatgggcaagcagggagttagaacgattcgcagttaatcctggcctattagaaacatcagaaggctgtagacaaatactgggacagctacaaccagct---cttcagacaggatcagaagaacttaaatccttatataatacagta---gcaaccctctattgtgtgcatcaaaagatagatgtaaaagacaccaaggaagctttagaaaagatagaggaagagcaaaacaaaagtaag------------------------aaaaaagcacagcaagcaacagct---------------gcagctgacacagga------------------aac---agcagccag------------------------gtcagccaaaattaccctata------------gtgcagaacctccaggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgggtaaaagtagtagaagaaaag------gctttcagcccagaagtaatacccatgttttcagctttatcagaaggagccaccccacaagatctgaacaccatgttaaacacagtggggggacatcaa---gcagccatgcagatg---ttaaaagag---accatcaatgaggaagctgcagaatgggatagattgcat---ccagtgcatgca---gggcctattgcaccaggccagatg---agagaaccaaggggaagtgacatagcaggaactactagtaac---cttcaggaacaaataggatggatgaca---------aataatcca---cct---atc---ccagta---ggagaaatctataaaagatggataatcctgggattaaataaaatagtaaggatgtatagccctaccagcattctggacataaaacaaggaccaaaggaaccctttagagactatgtagaccggttctataaaactttaagagccgagcaagcttcacaggaagtaaaaaattggatgacagaaaccttgttggtccaaaattcgaacccagattgtaagactattttaaaagcattgggaccagcggctacactagaagaaatgatgacagcatgtcagggagtgggaggacccggtcataaa---gcaagagttttggcggaa------gcaatg---agtcaagtaacaaat---------------------tcaaataccata---atgatg------cagaaaggcaac---------ttt---aggaaacaaagaaag------actgttaagtgtttcaattgcggcaaagaaggg---cacatagccagaaattgcagggcccctaggaaaaggggctgttggaaatgtggaaaggaaggacatcaaatgaaagattgt---------------actgaaagacaggctaattttttagggaagatctggcc---ttcccacaa------ggg---aag---gccagggaattttcttcagagcagaccagagccgacagc------------------------------------------------------cccaccaga------agagagcttcaggtt------------tggggaagagacaacaac---gccctc------------------------------tcagaa---------------acaggatct------gatagacttagacaa---------------------------gga------------actgca------tcctttagcttccctcagatcactctttggcaacgaccccttgtcgaaataaagataggggggcaactaaaggaagctctattagatacaggagcagatgatacagtatta---gaagaa---atgaatttgccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcaggtactcatagaaatctgtggacataaagctataggtacagtgttagtaggacctacacctgtcaac---ataattgggagaaatctgttgactcagattggttgcactttaaattttcctattagtcatattgacactgtgccagtaagattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aagataaaagcattagtagaaatctgtaca------gaaatggaaaaagaagggaaaatttcaaaa---attgggcct---gaaaatccatacaatactccagtatttgccataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagagaacttaataagaagactcaagatttctgggaa---gttcaa------tta---ggaata---------------------------ccacatcctgcagggttaaaaaagaaa---aaa------tcagtaacagtactggatgtgggtgatgcatat---ttttcagttcccttagataaagaattcaggaagtatactgcattcaccatacctagtataaacaatgagacaccagggattagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatcttagagccttttagaaaacaaaatccagacatagttatctatcaatacatggatgatttgtatataggatctgacttagaaatagggcagcatagaacaaaaatagaggaactgagacaacatctgctgaggtggggattcaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccaaac---aaagac---agctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatctacccagggattaaagtaaaacaattatgtaaactccttaggggaaccaaggcactaacagaagtaataccactaacaaaagaagcagagctagaactggcagaaaacagggaaattctaaaagaaccagtgcatggagtgtactatgacccagcaaaagacttgatagcagaaatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatgcaagaatg---aggggtgcccacactaatgatgta------agacaattaacagaggcagtgcaaaaaatagtcacagaaagtatagtaatatggggaaag---agtcctaaatttaaactacccatacaaaaagaaacatgggaaacatggtggacagagtattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagtgaaattatggtaccagttagagaaagaacctataataggagcagaaactttctatgtagatggggcagctaacagggagactaaattaggaaaagcaggatatgttactaatagagggaggcaaaaa---gttgtctccctaactgacacaacaaatcagaagactgaattacaagcaattcatctagcgttgcaggattcgggattagaag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+>B.US.11.VC6_2.KF384814
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+>B.US.12.2302_PBEM_13.KY778473
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+>B.US.12.2452_PBEM_13.KY778615
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+>B.US.12.409_133_F_w02VT.MH897911
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+>B.US.12.420_133_F_w02_10VT.MH897913
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+>B.US.12.421_34_F_w01VT.MH897915
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+>B.US.12.505_0772a.WG2.MG196819
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+>B.US.12.505_1413a.WG05.MG197046
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+>B.US.12.505_1569a.WG11.MG197055
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+>B.US.12.607523.KT124784
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+>B.US.12.608647.KT124785
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+>B.US.12.N8261_FL_CON.KU901976
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+>B.US.12.T8250_FL_CON.KU901997
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+>B.US.13.2115_EM_19.KY778345
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+>B.US.13.2275_EM_21.KY778395
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+>B.US.13.439_133_F_w11VT.MH897918
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+>B.US.13.505_0280a.WG04.MG196711
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+>B.US.13.862898.KT124796
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+>B.US.13.ARC_1a.MK214316
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+>B.US.13.CP02.KX505589
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+>B.US.13.CP03.KX505616
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+>B.US.13.CP06.KX505652
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+>B.US.13.CP07.KX505686
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+>B.US.13.G4_RV_1.KT284371
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+>B.US.13.S1492_T1_Intact.MG171201
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+>B.US.14.2046_EM_26.KY778299
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+>B.US.14.2286.KX505396
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+>B.US.14.2529.KX505475
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+>B.US.14.2531.KX505508
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+>B.US.14.Pt2_DNA_28.KU678026
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+>B.US.15.2521.KX505446
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+>B.US.15.3693.KX505555
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+>B.US.15.454_34_F_w01VT.MH897920
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+>B.US.15.UNC_308_PL1_A14.MW062426
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+>B.US.16.2609.KX505536
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+>B.US.16.2647_TTM_30.MN467271
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+>B.US.16.3632_TCM_12.MN466965
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+>B.US.16.5104_GAG_CD69_F10.MT189316
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+>B.US.16.5106_GAG_NEG_B5.MT190989
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+>B.US.16.603_Q3_H9.MT189857
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+>B.US.16.9245_W0_2A22_S84.MK115360
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+>B.US.16.9246_W0_1H8_S31.MK115401
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+>B.US.16.9247_CEFT_CD69_L18.MT190008
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+>B.US.16.9252_W0_16I9_S79.MK115745
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+>B.US.16.B207_CMV_CD69_G13.MT190767
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+>B.US.16.PID1683.PBMC_M18_03_WIPF1_F1F4_PBio.MN691961
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+>B.US.16.VA40774.MK499378
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+>B.US.17.UNC_367_PL1_I17.MW062703
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+>B.US.18.114_LN_6F22.MK169493
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+>B.US.18.120_LN_2_A6.MK169677
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+>B.US.18.5101_wk_2_5_G24.MW059247
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+>B.US.18.5111_wk_2_PL3_G16.MW059483
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+>B.US.18.5114_wk_2_PL5_I17.MW059651
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+>B.US.18.5203_wk_2_4_B21.MW059684
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+>B.US.18.TSC_125V1_PL2_H10.MW063070
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+>B.US.18.UNC_434_PL1_D2.MW062926
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+>B.US.18.UNC_437PL5_A16.MW062962
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+>B.US.83.5018_83.AY835777
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+>B.US.85.Ba_L.AB221005
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+>B.US.86.5096_86.AY835749
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+>B.US.86.5127_86.AY835774
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+>B.US.86.AD87_ADA.AF004394
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+>B.US.86.JRFL_JR_FL.U63632
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+>B.US.90.US1.AY173952
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+>B.US.90.US2.AY173953
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+>B.US.90.WCIPR.U69591
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+>B.US.91.5048_91.AY835761
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+>B.US.91.DH12_3.AF069140
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+>B.US.94.5082_94.AY835773
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+>B.US.95.5073_95.AY835768
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+>B.US.95.Pt9_1995_9.KU678164
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+>B.US.96.5155_96.AY835753
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+>B.US.97.1006_08.AY331284
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+>B.US.97.1051_11.KT124744
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+>B.US.97.1053_06.KT124745
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+>B.US.98.98USHVTN1925c1.AY560107
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+>B.US.98.WC3_0498_4.EF175212
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+>B.US.99.284160.KT124759
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+>B.US.99.489910.KT124776
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+>B.US.x.119409_B05.MT033734
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+>B.US.x.1229I.FJ469685
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+>B.US.x.153202_A01.MT033853
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+>B.US.x.AC160_T9_Day_1034_Dom.EU616649
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+>B.US.x.AC_16_0_Days_Consen_fa.DQ127537
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+>B.US.x.CR0050Z.FJ469692
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+>B.US.x.CR0059T.FJ469694
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+>B.US.x.CR0127W.FJ469699
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+>B.US.x.CR0164U.FJ469702
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+>B.US.x.CR0192W.FJ469704
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+>B.US.x.CR0206U.FJ469705
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+>B.US.x.CR0234.FJ469711
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+>B.US.x.CR0248X.FJ469712
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+>B.US.x.CR0317N.FJ469719
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+>B.US.x.CR0382N.FJ469725
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+>B.US.x.CR0413T.FJ469726
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+>B.US.x.F701.FJ469727
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagtgcgggggaattagataaatgggaaaaaattcggtta---agg------cca---ggaggaaagaaaaaatataggttaaaacatatagtatgggcaagcagggagctagaacgatttgcagttaatcctggcctgttagaaacagcagagggctgtaaacaaatattgggacaactacaatcatcc---cttcagacaggatcagaagaacttaaatcattgtttaatctagta---gcagtcctctggtgtgtgcatcaaaagatagatgtaaaagacactaaggaagctttagataagatagaagaagagaaaaacaaaagcaag------------------------aaaaaggcacagcaagcagcagct---------------------gacacagga------------------aac---agcaaccag------------------------gtcagccaaaattaccctata------------gtgcaaaacctacaggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgggtaaaagtagtagaagaaaag------gctttcagcccagaagtaatacccatgtttgcagcattatcagaaggagccaccccacaagatttaaacaccatgttaaacacagtggggggacatcag---gcagccatgcaaatg---ttaaaagag---accatcaatgaggaagctgcagaatgggatagattgcat---ccagtgcatgca---gggcctattgcaccaggccagatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaataggatggatgaca---------agcaatcca---cct---atc---caagta---ggagagatctataaaagatggataatcctgggattaaataaaatagtaaggatgtatagtcctaccagcattctggatataagacaaggaccaaaggaaccctttagagattatgtagaccggttctataaaactctaagagccgagcaagctacacaggaggtaaaaaattggatgacagaaaccttgttggtccaaaatgcaaacccagattgtaagaccattttaaaagcattaggaccagcagctacactagaagaaatgatgacagcatgtcagggagtgggaggacctggccataaa---gcaagagtcttggctgaa------gcaatg---agccaagtaacaaat---------------------tcacctgccata---atgatg------cagaggggcaat---------ttt---aggaaccaaagaaag------actgttaaatgtttcaattgtggcaaagaaggg---cacatagccaaaaattgcagggcccctaggaaaaagggctgttggaaatgtggaagggaaggacaccaaatgaaagactgt---------------actgagagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---aag---gccagggaattttcctcagagcaagatagagccaacagc------------------------------------------------------cccaccaga------agagagcttcaggtt------------tggggaggagacaacaac---tccccc------------------------------tcagaa---------------gcaggagcc------------gatagacaa---------------------------gga------------actata------tcctttagcttccctcagatcactctttggcaacgacccctcgtcacaataaagataggggggcaaacaaaggaagctctattagatacaggagcagatgatacagtatta---gaagac---atgagtttgccaggaagatggaagccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcaggtagccatagaaatctgtggacataaagctataggtacagtattaataggacctacacctgtcaac---ataattggaaggaatctgttgactcagattggttgcactttaaattttcccataagtcctattgaaactgtaccaataaaattgaagccaggaatggatggcccaaaagttaaacaa---tggccattaacagaagaa---aaaataaaagcattagtagaaatttgtaca------gaaatggaaaaggaagggaaaatttcaaaa---attgggcct---gaaaatccatacaatactccagtatttgctataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagagagcttaataagagaactcaagacttctgggag---gttcaa------tta---ggaata---------------------------ccacatcccgcagggttaaaaaagaaa---aag------tcagtaacagtactagatgtgggtgatgcatat---ttctcagttcccttagatgaagacttcaggaagtatactgcattcaccatacctagtataaacaatgagacaccagggattagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatcttagatccttttagaaaacaaaatccagacatagttatatatcaatacatggatgatttgtatgtaggatctgacttagaaatagggcagcatagaacaaaagtagaggaactgagacatcatctgttgaagtggggattcaccacaccagacaaaaagcatcagaaagaacctccattcctttggatggggtatgaactccatcctgataaatggacagtacagcctataaaactgccagaa---aaggac---agctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttacccagggattaaagtaaagcaattatgtaaactccttaggggtaccaaagcattaacagaagtaataccactaacagaagaagcagaactagaactggcagaaaacagggagattctaaaagaaccagtacatggggtgtattatgacccatcaaaggaattaatagcagaaatacagaagcagggggaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatgcaagaatg---aggggtgcccacactaatgatgta------aagcaattaacagaggcagtgcaaaaagtagccctagaaagcataataatatggggaaag---actcctaaatttagactacccatacaaaaagaaacatgggaaacatggtggacagattattggcaagccacctggattcctgagtgggagtttgtcagtacccctcccttagtaaaattatggtaccagttagagaaagaacccatagtaggagcagaaactttctatgtagatggggcagctaacagggatactaaagcaggaaaagcaggatatgttactgacagaggaagacaaaaa---gttatctccctaactgacacaacaaatcagaagactgagttacaagcaattcatttggctttgcaggattcaggagtagaag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+>B.US.x.F703.DQ886031
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+>B.US.x.F710.FJ469729
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+>B.US.x.F7174.DQ886032
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattacgcgggggacaattagatacttgggaaaaaattcggtta---agg------cca---gggggaaagaaacaatatcgcttaaaacatctagtatgggcaagcagggaactagaacgattcgcaattaaccctggcctgttagaaacagcagagggctgtagacaaataataggacaattacaaccagcc---cttcagacaggatcagaagaagtcaaatcattatttaatacagta---gcaaccctctattgtgtacatcaaaacatagaagtaagagacaccaaggaagctttagataagatagaggaagagcaaaacaaaagtaag------------------------aaaaaggcacagcaagcagcagct---------------------gacacagga------------------aac---agcagccag------------------------gtcagccaaaattaccctata------------gtgcagaatctacaggggcaaatggtacatcaggccataacacctagaactttaaatgcatgggtaaaagtagtagaagagaag------gcttttagcccagaagtaatacctatgttttcagcattatcagaaggatgcaccccacaagatttaaacctcatgctaaacacagtggggggacatcaa---gcagccatgcagatg---ttaaaagaa---accatcaatgaggaagctgcagaatgggatagaatgcat---ccagtgcaggca---gggcctgttgcaccaggccagata---agagaaccaaggggaagtgacatagcaggaactactagtaac---cttcaggaacaaataacatggatgaca---------agtaatcca---cct---atc---ccagta---ggagaaatctataaaagatggataatcctgggattaaataaaatagtaagaatgtatagtcctaccagcattctggacataaggcaagggccaaaggaaccctttagagactatgtagacaggttctataaaactctaagagccgagcaagcttcacaggaagtaaaaaattggatgacagaaactttgttggtgcaaaatgcaaacccagattgtaaaactattttaaaagcattgggaccagcagctacactagaagaaatgatgacagcatgtcagggagtggggggacccggacataaa---gcaagagtcttggctgaa------gcaatg---agccaagtaacaaat---------------------ccagctgccata---atgatg------cagaaaggcaat---------ttt---aggcaccaaagaaaa------actgttaagtgtttcaattgtggcaaagaaggg---cacatagccaaaaattgcagggcccctaggaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagattgt---------------actgagagacaggctaattttttagggaaaatctggcc---ttcccgcag------ggg---ggg---gccaggaaattttcctcagggcagactagagccaacagc------------------------------------------------------cccaccaga------ggagagcttcaggtt------------tggagaagagacaacaac---tccccc------------------------------tcagaa---------------gcaggaccc------------gatagacaa---------------------------gga------------gatgta------tcccttagcttccctcagatcactctttggcaacgacccctcgtcacaataaaggtaggggggcaactaaaggaagctctattagatacaggagcagatgatacagtatta---gaagaa---atgaatttgccaggaagatggaaaccaaaaatgatagggggaattggaggctttatcaaggtaagacagtat---gatcaggtatccatagaaatctgtggacataaagctatagggacagtattagtaggacctacacctgtcaac---ataattggaagaaatctgttgactcagattggttgcactttaaattttcccattagtcctattgaaactgtacctgtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaagcattagtagaaatttgtaca------gaaatggaaaaggaaggaaaaatttcaaaa---attgggcct---gaaaatccatacaatactccagtatttgccataaggaaaaaagacagt------accaagtggagaaaattagtagatttcagagaacttaataagagaactcaagacttttgggaa---gttcaa------cta---ggaata---------------------------ccacatcctgcagggttaaagaagaaa---aaa------tcagtaacagtactggatgtgggtgatgcatat---ttctcagttcccttagatgaagatttcaggaagtatactgcatttaccatacctagtataaacaatgagacaccagggattagatatcagtacaatgtgcttccacagggatggaagggatcaccagcaatattccaaagtaccatgacaaaaattctagagccttttaggaaacaaaatccagacatagttatctatcagtacatggatgatttgtatgtaggatctaacttagaaataggacagcatagaacaaaaatagaggaactgagacaacatctgttgaggtggggacttaccacaccagacaaaaaacatcagaaagagcctccattcctttggatgggttatgagctccatcctgataagtggacagtacagcctatagagctgccagaa---aaagaa---agctggactgtcaatgatatacaaaagttagtggggaaattgaattgggcaagtcagatttacgcaggaattaaagtaaagcaactatgtagactcctgaggggaaccaaagcactaacagaagtaataccactaacagaagaagcagagctagaactagcagaaaacagggagattctaaaagaaccagtacatggagtgtattatgacccatcaaaagaattaatagcagaaatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaagtatgcaagaatg---aagggtgcccacactaatgatgta------aaacaattaacagaggcagtgcaaaaaataagcgcagaaagcatagtaatatggggaaag---actcctaaatttagactacccatacaaaaagagacatgggaagcatggtggacagagtattggcaagccacctggattcctgagtgggagtttgttagtacccctcctctagtaaaattatggtaccagttagagaaagaacccataggaggagcagaaactttctatgtagatggggcagctaataaagagactaaattaggaaaagcaggatatgttactgacagaggaaggcaaaag---gttgtctccctagctgacacaacaaatcagaagactgagttacaagcaattcatctagctttgcaggattcagaattagaag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+>B.US.x.F7204.DQ886033
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tgcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggagaattagataaatgggagaaaattcggtta---agg------cca---ggaggaaggaaacaatataaattaaaacatatagtatgggcaagcagggagctagaacgattcgcagttaatcctggcctgttagaaacatcagagggctgtagacaaatactgggccagctacaaccatcc---cttcagacaggatcggaagaacttaactcattatctaatacaata---gcagtcctctattgtgtacatcaaagaatagacataaaagacaccaaggaagctttagacaagatagaggaagagcaaaacaaaagtaag------------------------aaaaaagtacagcaagcagcagct---------------------gacacagga------------------aac---agcaaccag------------------------gtcagccaaaattaccctata------------gtacagaatgtccaggggcaaatggtacatcaagccatatcacctagaactttaaatgcatgggtaaaagtagtagaagagaag------gctttcagcccagaagtgatacccatgttttcagcattatcagaaggagccaccccaagcgatttaaataccatgttaaacacagtggggggacatcaa---gcagctatgcaaatg---ttaaaagag---accatcaatgaggaagctgcagaatgggatagattgcat---ccagtgcatgca---gggcctattgcaccaggccagatg---agagaaccaaggggaagtgatatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------aataatcca---cct---atc---ccagta---ggagacatctataaaagatggataatactaggattaaataaaatagtaaggatgtatagtcctaccagcattttggacataagacaaggaccaaaggaaccctttagagactatgtagaccggttctataaaactctaagagccgagcaagcttcacaggatgtaaaaaattggatgacagaaaccttgttggtccaaaatgcgaacccagattgtaagactattttaaaagcattaggaccagcagctacactagaagaaatgatgacagcatgtcagggagtgggaggacctggccataaa---gcaagagttttggctgaa------gccatg---agccaagcatcaaat---------------------gcaactaacata---atgatg------cagagaggcaat---------ttt---aggacccagagaagg------attgttagatgtttcaattgtggcaaagaaggg---cacatagccaaaaattgcagggctcctagaaaaaagggctgttggagatgtggaaaggaaggacaccaaatgaaagattgc---------------tctgagagacaggctaattttttagggaagatctggcc---ttcccacaa------ggg---gag---gccagggaattttcttcagagcagaccagagccaacagc------------------------------------------------------cccaccaga------ggagagcttcaggtt------------tggggaggagac---aac---tccccc------------------------------tcagaa---------------gcaggaggc------------gatagacaa---------------------------gga------------actgta------tcctttagcttccctcaaatcactctttggcagcgacccctcgtcacaataaagataggggggcaactaaaagaagctctattagatacaggagcagatgacacagtatta---gaagaa---atgaatttgccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcagatacccatagaaatctgtggacatagagctataggtacagtattaataggacctacacctgtcaac---ataattagaagaaatctgttgactcagattggttgcactttaaattttcccataagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaagcattaatggaaatttgtaca------gaaatggaaaaggaaggaaaaatttcaaga---attgggcct---gaaaatccatacaatactccagtgtttgccataaagaaaaaggacagc------actaaatggagaaaattagtagatttcagagaacttaataagaaaactcaagacttttgggaa---gttcag------tta---ggaata---------------------------ccacatcccgcagggttgaaacagaaa---aaa------tcagtaacagtactagatgtgggtgatgcatat---ttttcagttcccctagataaagacttcaggaagtatactgcatttaccatacctagtataaataatgagacaccagggattagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaatgtagcatgacaaaaatcttagaaccttttaggaagcaaaatccagacatagttatctatcaatacatggatgatttgtatgtaggatctgacttagaaatagggcagcatagaacaaaaatagaggaactgagacaacatctgttaaggtggggatttaccacaccagacaaaaaacaccagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccagac---aaagac---agctggaccgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttacgcagggattaaagtaaggcaattatgtaaactccttaggggagccaaagcactaacagaagtagtaccactaacagaagaagcagagctagaactggcagaaaacagggaaattctaaaagaaccagtgcatggagtgtattatgacccatcaaaagacttaatagcagaaatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaagaatctgaaaacaggaaaatatgcaagaatg---aggggtgcccacactaatgatgta------aaacaattaacagaggcagtgcaaaaaatatccacagaaagcatagtaatatggggaaag---actcctaaatttagactacctatacaaaaaaaaacatgggaatcatggtggacagactattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagtgaaattatggtaccagttagaaaaggaacccataataggagcagaaactttctatgtagatggggcagctaacagagagactaaattagaaaaagcaggatatgttactaacagaggaagacaaaag---gttgtctccctaactgacacaacaaatcagaagactgagttacaagcaatttatttagctttgcaggattcaggattagaag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+>B.US.x.L8146.DQ886034
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+>B.US.x.L8157.DQ886035
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggagaattagatagatgggaaaaaattcggtta---agg------cca---gggggaaagaaaaaatatagattaaaacatatagtatgggcaagcagggagctagaacgatttgcagttaaccctggcctattagaaacatcagaagggtgtagacaaatactgggacagttacaaccatcc---cttcagacaggatcagaagaacttagatcattatataatacagta---gcaaccctctattgtgtgcatcaaaagatagatgtaaaagacaccaaggaagctttagagaaggtagaggaagagcaaaacaaaagtaag------------------------aaaaaggcacagcaagcagcagct---------------------gacacagga------------------aac---agcagcaag------------------------gtcagccaaaattaccctata------------gtgcagaacctccaggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgggtaaaagtagtagaagaaaag------gctttcagcccagaagtaatacccatgtttgcagcattatcagaaggagccaccccacaagatttaaacaccatgctaaacacagtggggggacatcaa---gcagccatgcagatg---ttaaaagag---accatcaatgaggaagctgcagaatgggatagattgcat---ccagtgcatgca---gggcctgttgcaccaggccagatg---agagaaccaaggggaagcgacatagcaggaactactagtacc---cttcaagaacaaataggatggatgaca---------aacaatcca---cct---acc---ccagta---ggagaaatctataaaagatggataattttggggttaaataaaatagtaaggatgtatagccctacctgcattttggacataaaacaaggaccaaaggaaccctttagagactatgtagaccggttctataaaactctaagagccgagcaggcttcacaggaggtaaaaaactggatgacagaaaccttgttggtccaaaattcgaacccagattgtaagactattttaaaagcattgggaccagcagctacactagaagaaatgatgacagcatgtcagggagtgggaggacccggccataaa---gcaagagttttggcagaa------gcaatg---agccaagtaacaaat---------------------tcagctaccata---atgatg------cagaaaggcaat---------ttt---agaaaccaaagaaaa------actgttaagtgtttcaattgcggcaaagaaggg---cacatagccagaaattgcagggcccctaggaaaagaggctgttggaaatgtggaaaggagggacaccaaatgaaagattgt---------------actgagagacaggctaattttttagggaagatctggcc---ttcccacaa------ggg---aag---gccagggaattttcttcagagcagaccagagccaacagc------------------------------------------------------cccaccaga------agagagcttcaggtt------------tggggaagagacaccaac---tccctc------------------------------tcagaa---------------gcaggagcc---gctgatagacttagacaa---------------------------gga------------actcct---gtatcctttagcttccctcagatcactctttggcaacgacccctcgtcgaaataaagataggggggcaaataaaggaagctctattagatacaggagcagatgatacagtatta---gaagaa---atgaatttgccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcagatactcatagaaatctgtggacataaaactataggtacagtattagtaggacctacacctgtcaat---ataattggaagaaatctgttgactcagattggttgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccgagagttaaacaa---tggccattgacagaagaa---aaaataaaagcattaatagaaatctgtaca------gaaatggaaaaagaagggaaaatttcaaaa---attgggcct---gaaaatccatacaatactccagtatttgccataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagagaacttaataagaaaactcaagacttctgggaa---gttcaa------tta---ggaata---------------------------ccacatcctgcagggttgaaaaagaaa---aaa------tcagtaacagtactggatgtgggtgatgcatat---ttttcagttcctttagataaagaatttaggaagtatactgcatttaccatacctagtacaaacaatgagacaccagggattagatatcagtacaatgtgcttccacaaggatggaagggatcaccagcaatatttcaaagtagcatgacaaaaatcttagagccttttagaaaacaaaatccagacatagttatctatcaatacatggatgatttgtatgtaggatctgacttagaaatagggcagcatagaacaaaaatagaggaactgagacaacatctgttgaggtggggatttaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaattgacagtacagcctatagtggtgccagaa---aaagac---agctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttacccagggattaaagtaaagcaattatgtagactccttaggggaaccaaggcactaacagaagtaataccactaacaaaagaagcagagctagaactggcagaaaacagggaaattttaaaagaaccagtacatggagtatattatgacccaacaaaagacttaatagcagaaatacagaagcaggggcacggccaatggacatatcaaatttatcaagaaccatttaaaaatctgaaaacaggaaaatatgcaagaatg---aggggtgcccacactaatgatgta------aaacaattaacagaggcagtgcaaaaaatagccacagaaagcatagtaatatggggaaag---attcctaaatttaaactacccatacaaaaagaaacatgggagacatggtggacagagtattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagtgaaattatggtaccagctagagaaagaacccataataggagcagaaactttctatgtagatggggcagcaaacagggagactaaagtaggaaaagcaggatatgttactaacagagggagacaaaaa---gttgtctccctaactgacacaacaaatcagaagactgagttacaagcaattcatctagctttacaggattcaggattagaag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+>B.US.x.L8185.DQ886036
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+>B.US.x.L8188.FJ469744
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+>B.US.x.L896.FJ469750
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+>B.US.x.NCQ.FJ469752
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+>B.US.x.PRLS05.FJ469756
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+>B.US.x.PRLS17.FJ469761
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+>B.US.x.PRLS19.FJ469763
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+>B.US.x.PRLS28.FJ469766
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+>B.US.x.SH8127.FJ469767
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+>B.US.x.SH8183.FJ469768
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+>B.US.x.SH8229.FJ469769
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+>B.US.x.SH8241.FJ469771
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+>B.US.x.sample_C_BID_D617.JX503075
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+>B.ZA.09.DEMB09ZA022.KP109515
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+>B.x.00.LA02FolC.KU168257
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+>B.x.02.LA03BlEr.KU168258
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+>B.x.02.LA04GuFu.KU168259
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+>B.x.03.LA05MeAl.KU168260
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+>B.x.10.DEURF10HA002.KY658703
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+>B.x.x.HypervirulentDutchHIV_1.MT458931
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tcttgggagcagca---ggaagcactatgggcgcagcgtca---gtaacgctgacggtacaagcc---agg------cag---ttattg---tctggtatagtgcaacagcaa---aacaacttg---ctgagggctattgaggcgcaacagcatatgttgcaactcacagtctggggcattaagcagctccag---gcaagagtcctggctgtggaaagatacctacaggatcaacagctcctggggatttggggttgctctggaaaactcatttgcaccactgctgtgccttggaatgct---agt---tgg------------------------------------agtaataaaaatctaagtcaaatttgg---------gat---aacatgacctggatgcag---tgg---gaa-aaggaaattgacaattacacaggagtaatatatgacttacttgaaaaatcacag-aaccagcaagaa-aagaatgaacaagaattattggaattggataaatggacaaatttgtggagttggtttgacataacaaactggctgtggtatata-agactattcataatgatagtaggaggcttaataggttta-agaatagtttttgctgtactttctatagtgaaaagagttaggcagggatactcaccactatcg---tttcag---acccgcctcccagcc------cagagggga------cccgacagg------cccgaagaaaccgaagaagaaggtggagacagaaacagaggtggatccagtccattagtgcatggattcttagcaatcatctgggtcgacctgcggagcctgtgcctcttcagctac---caccgcttgagagacttactcttgattgctgcgagggttgtggaa---ctt---ctg---ggacgc---------------------------------------------agggggtgg------gaagccctcaaa---tatctg---------tggaatctcctacagtattggggccaggaactaaagaatagtgct--attagtttgtttaatgccacagctatagcagttgctgag-gggacagataggattatagaagtagcacaaagaatttttaga------gctattatccacatacctaga---agaataagacagggcttggaaagggct------ttg-------caa---taa--------------------------------------gatgggtggcaaggggtcaaaa------------atg---gctgccggatggactagagtaagggacagaatgagacgagca---------------------------------------------------ccagcaaatgaaccagca------------------------------gcagagggggtgggagca---gtatctcgagacctggaaagacatggagcaatcacaagtagcaatacagcatctgct------gct---tgtacatggctagaagca---------caagagcaa---------gag---gaggaggtgggctttccagtcagacctcaggtacctttaagaccaatgacttataagggagctctg------gatcttagccactttttaaaagaaaaggggggactg---gaagggctaatttactcccagcaaagacaagatatc---------cttgatctgtgggtctacaacaca-caa---ggctacttccctgattggcag---aactacacaccagggccagggatcagatatccactgtgctttggatggtgctttaagctagtaccagttgaaccagagaagatagaagag------ctcactcaagga------gagaacaactgcttgttacatcctgcaaaccagcatggaatggatgaccca---gagaag---gaagtattaatgtggaagtttgacagccgcctggca-tttcatcacatggcccgagagaagcat---ccggagttt------------------------tacaacaacaactaaagactgctgac-------------------------------atcgagctt-------------------------tctacaa----------------------------------------gggactttcc----------------gctg---------------------------------------gggactttcc--------------------------------------------------------------------------------aggggaggt------------gtggcc-tgggcgggacc-----------gggg-agtg-gc-ga----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------g----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>B.x.x.HypervirulentDutchHIV_3.MT458933
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------g-ctagc-taggg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-ttt--aa-g-----ta-gtgt-gtgcccatctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagacacct-ttag-t-cagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------cagaaaacgaaag------------------------------------------tagaaccggagga--------gatctctcgacgca-ggactcggcttgct---gaagcgcgcacagcaagaggc-------------gagg-gg--cggc-----gactggtgagtacgcc------------------------aaattttttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcggcggaaaattagaccattgggaaaaaattcggtta---cgg------cca---gggggaaagaaacaatatagactaaaacatatagtatgggcaagcagggagctagaacgatttgcacttaatcctgcactgttagaaacagcagagggctgtagacagatactgggacagctacaaccagcc---cttcagacaggatcagaagaacttaaatcattacataatacagta---gcaaccctctattgtgtacatctaaggatagatgtaaaagacaccaaggaagctttagattacatagaggaagagcaaaacaaaagtaag------------------------aaaaagatacagcaagcagcagct---------------------gccacagga------------------aac---agcagccag------------------------ggcagccaaaattaccctata------------gtgcagaatctacaggggcaaatggtacatcaggcaatatcacctagaactttaaatgcatgggtgaaagtaatagaagagaag------gctttcagtccagaagtgatacccatgttttcagcattatcagagggagccaccccacaagatttaaacaccatgctaaatacagtggggggacatcaa---gcagctatgcaaatg---ttaaaagag---accatcaatgaggaagctgcagaatgggacagactgcat---ccacagcaggca---gggcctgttgcaccaggccagatg---agagacccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaataaattggatgaca---------agtaatcca---cct---atc---ccagta---ggagaaatttacaaaagatggataattctgggattaaataaaatagtaagaatgtatagcccaaccagcattctagacataagacaaggaccaaaggagccctttagagactatgtggaccggttctataaaaccctaagagctgagcaagcttcacaggaagtaaaaaattggatgacagaaaccttgttggtccaaaattcgaacccagattgtaagactattttgaaagcattaggaccaggggctacactagaagaaatgatgacagcatgtcagggagtgggaggacctggccataaa---gcaagagttttggctgaa------gcaatg---agccaggtacaaaca------------------aatgcagctaacgta---atgatg------cagagaggcaat---------ttt---gggggccaaagaaaa------actgttaagtgtttcaattgtggcaaagtaggg---catatagctaaaaattgcagggcccctagaaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagattgt---------------actgagagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---gag---gccagggaattttcttcagaacagaccagagccaacagc------------------------------------------------------cccaccaga------agagagcttcaggtt------------tggggaggagacagcacc---tcctcc------------------------------tcagaa---------------gcaggagca------------gagagacag---------------------ggacaagga------------actata------tcccttagcctccctcagatcactctttggcaacgaccccttgtcacaataaaggtagggggacaactaaaggaagccctattagatacaggagcagatgatacagtatta---gaagaa---atgaatttgccagggagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcagatacccatagaaatctgtgggcataaagctataggtacagtattagtaggacctacacctgtcaac---ataattggaagaaatctgttgactcagattggttgtaccttaaattttcccattagtcctattgaaactgtacctgtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagag---aaaataaaagcattagtagaaatttgtaca------gaattagaaaaagaaggaaagatttcgaaa---attgggcct---gagaatccatacaatactccaatatttgctataaagaaaaaagacagt------actaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctgggaa---gttcaa------tta---ggaata---------------------------ccacatcccgcagggttaaaaaagaaa---aaa------tcagtaacagtactggatgtgggtgatgcttat---ttttcagttcctttagatgaagacttcaggaagtatactgcatttaccatacctagtacaaacaatgagacaccagggattagatatcaatacaatgtgcttccacagggatggaaaggatcaccagcaatatttcaaagtagcatgacaagaatattagaaccttttagaaaacaaaatccagacatagttatttatcagtacatggatgatttgtatgtaggatctgacttagaaataggacagcataggacaaaaatagaagaactgagacaacatctgttggggtggggatttaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccagaa---aaagac---agctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttatgcagggatcaaagtaaggcaattatgtaagctccttaggggaaccaaagcactaacagaagtagtaccactaacagtagaagcagagctagaactggcagagaacagggagattctaaaagagccagtacatggagtgtattatgacccatcaaaagacttaatagcagaaatacagaaacaagggcaaggccaatggacatatcaaatatatcaagagccatttaaaaatctgaaaacaggaaagtatgcaagaatg---aggggtgcccacactaatgatgta------aaacaattaacagaggcagtgcaaaaaatagccacagaaagcatagtaatatggggaaag---acccctaaatttagactacccatacaaaaagagacatgggaaatatggtgggcagagtattggcaggccacctggattcctgagtgggagtttgtcaatacccctcccttagtaaaattatggtaccagttagaaaaggaacccatagtaggagcagaaactttctatgtagatggggcagctaatagggaaactaaattaggaaaagcaggatatgttactgacagaggaaggcaaaag---gttatccccctaacagacacaacaaatcagaagactgagttacaagcaatttatctagctttacaggattcgggattagaag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+>C.BR.02.02BR2022.JN692434
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+>C.BR.04.04BR021.AY727523
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+>C.BR.04.04BR038.AY727524
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+>C.BR.04.04BR073.AY727525
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+>C.BR.10.DEMC10BR024.KU749392
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+>C.BR.11.DEMC11BR035.KU749393
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+>C.BR.17.6HU_FURG_2017.MK041561
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+>C.BR.17.8HU_FURG_2017.MK041564
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+>C.BW.00.00BW07621.AF443088
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+>C.BW.00.00BW076820.AF443089
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+>C.BW.00.00BW16162.AF443092
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+>C.BW.00.00BW1686.AF443093
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+>C.BW.00.00BW17593.AF443094
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+>C.BW.00.00BW192113.AF443101
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+>C.BW.00.00BW20361.AF443102
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+>C.BW.00.00BW20872.AF443104
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+>C.BW.00.00BW22767.AF443107
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+>C.BW.00.00BW38193.AF443108
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+>C.BW.00.00BW38713.AF443110
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+>C.BW.00.00BW3886_8.AF443112
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+>C.BW.00.00BW5031_1.AF443115
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+>C.BW.15.074_A_104_1_0_w0_353.MK458117
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+>C.BW.15.074_A_105_1_3_w0_68.MK457832
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+>C.BW.15.074_A_109_1_1_w0_276.MK458040
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+>C.BW.15.074_P_201_1_4_w0_30.MK457794
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+>C.BW.96.96BW15C02.AF110974
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+>C.BW.96.96BWM032.AF443075
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+>C.BW.98.98BWMC122.AF443076
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+>C.BW.98.98BWMC134.AF443077
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+>C.BW.98.98BWMO1410.AF443079
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+>C.BW.98.98BWMO18D5.AF443080
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+>C.BW.98.98BWMO36A5.AF443081
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+>C.BW.98.98BWMO37D5.AF443082
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+>C.BW.99.99BW4745.AF443085
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+>C.CN.09.09YNLX133sg.KC898996
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+>C.CN.09.DH21.KF250403
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+>C.DE.10.622166.KT124786
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+>C.DJ.x.DJ259.AB485643
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+>C.ES.07.Read4_HIV_C.KX228820
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+>C.ES.15.100_118.KY496624
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+>C.IL.98.98IS002.AF286233
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+>C.IN.00.DEMC00IN005.KP109480
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+>C.IN.00.DEMC00IN009.KP109484
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+>C.IN.03.D24.EF469243
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+>C.IN.04.C.IN.04.NIRT379.1.KF766537
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+>C.IN.05.C.IN.05.NIRT723.1.KF766541
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+>C.IN.09.T125_2139.KC156210
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+>C.IN.11.NIRT009.KX069227
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+>C.IN.11.NIRT010.KX069228
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+>C.IN.15.SC013.KY713230
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+>C.IN.15.SC062.KY713234
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gag-ggaggtt-aagg-gctccc-tgt-ctttcggc-tcctgcttcggaggag-ctggggttgtct--------------------------------cc-t-cgaacctgagggtccctgg-ctatc-taggg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-tct--ga-g-----ca-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagacc-ct-tgtg-gtagtgtggaaaaa-tctctagcagtggcg--------cccgaacagggac------------------ccgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-gggctcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--gggc-----gactggtgagtacgcc-----------------------aattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagagggggaaaattagataaatgggaaaaaattaggtta---agg------cca---gggggaaagaaacaatataggctaaaacatttagtatgggcaagcagggagctggaaaaatttgcacttaaccctgaccttatggagacatcagacggctgtaaacaaataataaaacagctacaaccagct---attcagacaggaacagaggaacttagatcattatacaacacaata---gcagttctctattgtgtacatgcaagagtagaagtaaaagacaccaaagaagccttagacaagatagaggaagaacaaaataaaattcag---------------------------------cagcaggcaaaagag---------------------gctgacagg------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtacaccagcccttatcacctaggactttaaatgcatgggtaaaagtaatagaggaaaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatctaaacaccatgttaaatacagtagggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaagaggctgcagaatgggatagattacat---ccagtacatgca---gggcctgttccaccaggccaaatg---agagagccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------agtaaccca---cct---gtg---ccagtg---ggagacatctataaaagatggataattctgggtttaaataaaatagtaagaatgtatagccctgttagcattttggacataagacaagggccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagagctgaacaagctacacaagaggtaaaaaattggatgacagacaccttgctggtccaaaatgcgaacccagattgtaggaccattttaaaagcattaggaccaggggctacattagaagagatgatgacagcatgtcagggagtgggaggacctggccacaaa---gcaagagtgttggctgag------gcaatg---agccaagcaaac---------------------------agtaacata---atgatg------cagaaaagcaat---------ttt---aaaggccctaaaaga---------gttaaatgtttcaactgtggcaaagaaggg---cacatagccagaaattgcagggcccctaggaaaaagggctgttggaagtgtggaaaggaaggacaccaaatgaaagactgt---------------actgaaaggcaggctaattttttaggaaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttcctccagagcagaccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---aac---cccagctcc---------------------------tccgaa---------------gcaggagcc------------gaaagacag---------------------------gga------------------------gcccttaacctccctcagatcactctttggcagcgaccccttgtcacaataaaagtagggggccagataaaagaggctctattggacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacaatat---gagcaagtacctatagaaatttgtggaaaaaaggctataggtacagtattagtaggacccacacctgtcaac---ataattggaagaaatatgttgactcagcttgggtgtacactaaattttccaattagtcccattgaaacggtgccagtaaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccactgacagaagag---aaaataaaggcattaatagaaatttgtgat------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacacaccaatctttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagatttttgggaa---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtgacagtactggatgtgggagatgcatat---ttttcagttcctttagatgaaagcttcaggaaatatactgcattcaccatacctagtacaaacaatgaaacaccagggattaggtatcaatataatgtgctcccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaaaatcttagagccctttagggcacggaatccagaactagtcatctatcaatatatggatgacttgtatgtaggatctaacttagaaataaagctacatagagcaaaaatagaagagttaagaggacatctgttaaagtggggatttaccacaccagacaagaaacatcagaaagaacctccatttctttggatggggtatgaactccaccctgacaaatggacagtgcagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacccaggaattaaagtaaggcaactctgtaaactccttaggggggccaaagcattaacagacatagtaccattaactgaagaagcagaattagaattggcagaaaacagggaaattctaaaagaaccagtacatggggtatattatgacccatcaaaggacttgatagctgaaatacagaaacaagggcaggaccaatggacatatcaaatttaccaagaaccattcaaaaatctgaagacagggaagtatgcaaaaatg---aggactgcccacactaatgatgta------aaacagttaacagaggctgtgcagaaaatatccatggaaagcatagtaatatggggaaag---actcctaaatttagattacccattcaaaaagaaacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggaatttgttaatacccctcccttagtaaaattatggtatcagctggagaaagatcccatagcaggagtagaaactttctatgtagatggggcagctaatagggaaactaaaatgggaaaagcagggtatgttactgacagaggaaggaagaaa---gttatttctctaactgaaacaacaaatcagaagactgaattgcaagcaatttatctagctttgctagattcaggatcagaag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+>C.IN.15.SC085.KY713235
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------a-gagccagagagctctctgg-ctatc-taggg------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-tca--ga-g-----ca-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagacactt-ttgg-t--agtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------gcgaaagcgaaag------------------------------------------taagaccagagaa--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--gggc-----gactggtgagtacgcc------------------------attttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagaggcgaaaaattagataaatgggaaagaattaggtta---agg------cca---gggggaaagaaatgttatcagctaaaacatatagtatgggcaagcagggagctggaaagatttgcacttaaccctggcctcttagaaacctcagaaggctgtaaacagataataagacagctacaaccagct---ctccagacagggacagaggaaattaaatcattacacaatgcagtg---tcaactctctattgtgtacatgcagggatagatgtaagagacaccaaggaagccttagacaagataaaggaggaacaagacagaatgcag------------------------caaaaagcacaacaggcaaaaggg---------------------gctgaaggg------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaacctccaagggcaaatggtacatcagcccatatcacctagaactttaaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacagtggggggacaccaa---gcagccatgcaaatg---ttaaaagac---accatcaatgaagaggctgcagactgggacagattacat---ccagtacatgca---gggcctattgcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------gctaaccca---cct---gtt---ccagtg---ggagaaatctataaaagatggataattctgggattaaataaaatagtaagaatgtatagccctagtagcattttggacataaaacaaggaccaaaggaacccttcagagattatgtagatcggttctttaaaactttaagagctgaacaagctacacaagaggtcaaaaattggatgacagacaccttgttggtccaaaatgcaaacccagattgtaagaccattctaagagcattaggaccaggggctacattagaagagatgatgacagcatgtcagggagtgggaggacctagccacaaa---gcaagagtgttagctgaa------gcaatg---agccaagcaaac---------------------------agctcagta---atgatg------cagagaggcaat---------ttc---aaaggccctaaaaga------actgttaaatgtttcaactgtggcaaggagggg---cacatagccagaaattgcagggcccctaggaaaaagggctgttggaagtgtgggaaagaaggacaccaaatgaaagactgt---------------actgaaagacaggctaattttttagggaaaatttggcc---ttcccacaa------gggggggag---gccagggaatttcctccagagcagaccagagccaacagc------------------------------cccaccgagactagagccaacagccccaccagc------agagagcttcaggtt------------cgggga---gac---aac---cccagc------------------------------cccgag---------------gcaggagca------------gaaggacag---------------------------gga------------------------gcccttaacctccctcagatcactctttggcagcgaccccttgtcccaataagaatagggggccagttaaaagaggctctcttagatacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggatttatcaaagtaagacaatat---gatcaaataccaatagaaatttgtggaaaaaaggcaataggtacagtattagtgggacccacacctatcaac---ataattggaaggaatatgttgactcagcttggatgcacactaaattttccaatcagtcccattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagaa---aaaatagaagcattaacagcaatttgtaat------gaaatggagaaggaaggaaaaatttcaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagatttctgggaa---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtgacagtactggatgtgggggatgcatat---ttttcagttcctttatatgaggacttcaggaaatatactgcattcaccatacctagtagaaacaatgaaacaccagggattaggtatcaatataatgtgcttccacagggatggaagggatcaccagcaatattccaggctagcatgacaaaaatcttagagccctttagagcaaaaaacccagaaatagtcatctatcaatacatggatgacttgtatgtaggatctgacttagaaatagggcaacatagagcaaaagtagaggaattaagagaacatctgttaaagtggggatttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggaa---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcaaatttacccaggaattaaagtaaggcaactttgtaaactccttaggggggccaaagcactaacagatgtaataccactaactgaagaagcagaattagaattggcagaaaacagggaaattttaaaagaaccagtacatggagcatattatgacccatcaaaagacttgatagctgaaatacagaaacaggggcaggatcagtggacatatcaaatttaccaagaaccattcaaaaatctgaaaacagggaagtatgcaaaaatg---aggactgcccacactaatgatgta------aaacagttaacagaggctgtgcagaaaatagccatggaaagcatagtaatatggggaaag---actcctaaatttagattacccatccaaaaagaaacatgggacacatggtggacagactattggcaagccacctggattccagagtgggaatttgttaatacccctcccttagtaaaattatggtatcagctagagaaagatcccatagcaggagtagaaactttctatgtagatggagcagctaacagggaaactaaactaggaaaagcagggtatgttactgacagaggaagacagaaa---attgtttctctaacagaaacaacaaatcagaagactgaattgcatgcaatttatctagccttgcaagattcaggatcagaag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+>C.IN.93.93IN101.AB023804
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+>C.IN.93.93IN904.AF067157
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+>C.IN.98.98IN012.AF286231
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+>C.IN.98.98IN022.AF286232
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+>C.IN.99.DEMC99IN001.KP109486
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+>C.IN.99.DEMC99IN002.KP109487
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+>C.IN.99.DEMC99IN004.KP109489
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+>C.KE.04.04KE585573V2.KT022366
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+>C.KE.05.05KE369195V4.KT022371
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+>C.MW.07.703010085_CH085.w4a.KC156211
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+>C.MW.07.703010131_CH131_TF.KC156114
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+>C.MW.07.703010167_CH167.w8.KC156213
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+>C.MW.07.703010200_CH200_TFc.KC156119
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+>C.MW.07.703010228_CH228_TFa.KC156120
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+>C.MW.08.4403bmLwk4_fl11.KF527172
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+>C.MW.08.702010432_CH432.w4.KC156218
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+>C.MW.08.702010440_CH440.w4.KC156219
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+>C.MW.08.703010269_CH269.w24.KC156215
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+>C.MW.08.CH455.PL.012908.UT.1.KY112254
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+>C.MW.08.DEMC08MW004.KP109522
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+>C.MW.09.703010256_CH256.w96.KC156214
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+>C.MW.09.CH1064.PL.080409.A2.08.KY111994
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+>C.MW.09.DEMC09MW006.KP109523
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+>C.MW.09.DEMC09MW007.KP109524
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+>C.MW.09.DEMC09MW008.KP109525
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+>C.MW.09.DEMC09MW009.KP109526
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+>C.MW.09.DEMC09MW010.KP109527
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+>C.NP.00.11NP115.KU341731
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+>C.NP.07.11NP091.KU341730
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+>C.SE.14.091SE.MF373193
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+>C.TH.14.2549734P000FL_Si.MG989567
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+>C.TZ.03.CO6980V0.KX907433
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+>C.TZ.10.30190v01_01.MN791903
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+>C.TZ.12.30812v01_01.MN791934
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+>C.ZA.00.1192M3M.AY463219
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+>C.ZA.00.1197MB.AY463234
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+>C.ZA.00.J112MA.AY838568
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+>C.ZA.00.J38MA.AY463228
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+>C.ZA.01.01ZATM45.AY228557
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+>C.ZA.01.J54Ma.AY463223
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+>C.ZA.02.02ZAPS001MB1.DQ275648
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+>C.ZA.02.02ZAPS005MB1.DQ351235
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+>C.ZA.02.02ZAPS006MB1.DQ351220
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+>C.ZA.02.02ZAPS013MB1.DQ351222
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+>C.ZA.03.03ZAPS024MB1.DQ396367
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+>C.ZA.03.03ZAPS026MB1.DQ369985
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccctt-tgtg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ccgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--gggc-----ggctggtgagtacgcc----------------------aatttttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagtgcgtcaatattaagaggcgaaaaattagagaaatgggaaaaaattaggtta---agg------cca---gggggaaagaaacattataggttaaaacacttagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacatcagaaggctgtaaacagataataagacagctacacccagct---cttcagacaggaacagaggaacttagatcattatataacacagtg---gcaactctctattgtgtacatgaaaagatagagatacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaattcag------------------------caaaaggcacagcaaacagaagtg------------------gctggcaaagga------------------------------aag------------------------gtcagtcaaaattatccaata------------gtgcagaacctccaagggcaaatggtacaccaggcattatcaccgagaactttaaatgcatgggtaaaagtaatagaggagaag------gccttcagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccacgttaaatacggtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaagaggcagcaggatgggatagattacac---ccagtacatgca---gggcctattgcaccgggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------agtaatcca---cct---att---ccagtg---ggagaaatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaagggccaaaggaaccctttagagattatgtagaccggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaacccagattgtaagaccattctaagagcattaggaccaggggccacattagaagaaatgatgacagcgtgtcaaggagtgggaggacctagccacaaa---gcaagagtgttggctgag------gcaatg---agccgaacaaac------------------------aatgtaaacata---atgatg------cagagaaacaat---------ttt---aaaggctctaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccagaaattgcagagcccctaggaaaaaaggatgttggaagtgtgggaaagaaggacaccaaatgaaagactgt---------------acggagaggcaggctaattttttagggaagatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagagcaggccagagccaacagc------------------------------------------------------cccaccggc------agagagcttcaggtt------------cgagga---gac---aac---ccccac------------------------------tccgaa---------------gcaggagcc------------gaaagacag---------------------------gga------------------------acccttaatttccctcaaatcactctttggcaacgaccccttgtctcaataagagtagggggccagataaaagaggctctcttagacacaggagcagatgatacagtatta---gaagat---ataaacttgccaggaaaatggagaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaaaggctataggtacagtattagtgggacctacacctgtcaac---ataattgggagaaacatgttgactcagcttggatgcacactaaattttccaattagtcccattgagaccgtaccagtaaaactgaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagaaatctgtaaa------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccgtataacactccaatatttgcaataaaaaagaaggacagt------gctaagtggagaaaattagtagatttcagggagcttaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcaggattaaaaaagaaa---aaa------tcagtgacagtactggatgtgggggatgcatat---ttttcagttcctttagatgaagactttagaaagtatactgcattcaccattcctagtataaacaatgaaacaccagggattagatatcaatataatgtacttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatcttagatccctttagagcaaaaaatccagaaatagtcatttatcaatatatggatgacttatatgtaggatctgacttagaaatagggcaacacagagcaaaaatagaggagttaagagcacatctattaaggtggggacttaccacaccagacaagaaacatcagaaagaacccccatttccttggatggggtatgaactccatcctgataaatggacagtacagcctattcagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcatgtcagatttatccagggattaaagtaaagcaaatttgtagactccttaggggagccaaagcactaacagacatagtaccactaactgaggaagcagaattagaattggcagagaacagggaaattctaaaagaaccagtacatggagtgtattatgacccatcaaaagaattaatagctgaaatacagaaacaggggcatgaccaatggacatatcaaatataccaagaaccattcaaaaatctgaaaacagggaaatatgcaaaaagg---aggacggcccacactaatgatata------aaacagttaacagaggcagtgcaaaaaatagctacagaaagcatagtaatccggggaaag---actcctaaatttagactacccatccaaaaagaaacatgggatatatggtggacagactattggcaagccacctggattccagagtgggagtttgttaatgcccctcccctagtaaaattatggtaccagctggagaaagaacccatagcaggagcagaaacattctatgtagacggagcagctaatagggaaactaaaatgggaagagcaggatatgttactgacaagggaaggcagaaa---attgtttctctaactgaaacaacaaatcagaaggctgagttacaagcaattcagctagctttgcaggattcaggatcagaag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+>C.ZA.03.03ZAPS042MB1.DQ369977
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+>C.ZA.03.03ZAPS044MB1.DQ396384
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+>C.ZA.03.03ZAPS048MB1.DQ396364
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+>C.ZA.03.03ZAPS049MB1.DQ369986
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+>C.ZA.03.03ZAPS050MB1.DQ369980
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+>C.ZA.03.03ZAPS051MB1.DQ396385
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+>C.ZA.03.03ZAPS052MB1.DQ369987
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+>C.ZA.03.03ZAPS066MB2.DQ396375
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+>C.ZA.03.03ZAPS073MB1.DQ275649
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+>C.ZA.03.03ZAPS077B1.DQ093591
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+>C.ZA.03.03ZAPS079B1.DQ093592
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccctt-gttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ccgaaagcgaaag------------------------------------------taggaccagagaa--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-gg--gggc-----gactggtgagtacgcc----------------------aaattttatttgact----------agcgga-gg---------ctagg-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgtgagagcgtcaatattaagagggggaaaattagataaatgggaaagaattaggtta---agg------cca---gggggaaagaaatgttatatgctaaaacacctagtatgggcaagcagggagctggaaagatttgcacttaaccctggtcttttagagacatcaaaaggctgtagacaaataatggaacagctacaaccagct---ctccagacaggatcagaggaacttaaatcattattcaacacaata---gcagttctctattgcgtacatgaagacatagaggtaagagacgccaaggaagccttagacaagatagaggaagaacaaaagaaaagtcag------------------------caaaaaacacagcaggcaaaagcg---------------------gctgacggg------------------------------aaa------------------------gtcagtcaaaattatcctata------------gtgcagaatcttcaagggcaaatggtacatcaggccatatcacctagaactttgaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacagtggggggacatcag---gcagccatgcagatg---ttaaaagat---accatcaatgaggaggctgcagagtgggatagagtacat---ccaatacatgca---gggcctgttgcaccaggccagatg---agggaacctagaggcagtgacatagcaggaaccactagtacc---cttcaagaacaaatagcatggatgaca---------agtaaccca---cct---gtc---ccagtg---ggagacatctataaaagatggataattctggggctaaataagatagtaagaatgtatagccctgttagcattttggacataaggcaagggccaaaggaaccctttagagactatgtagatcggttctttaaaactttaagagctgaacaagctacacaagaagtaaaaaattggatgacagacaccttgttgatccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccaggggcttcattagaagaaatgatgacagcatgtcagggagtgggaggacctagccacaaa---gcaagagtgttggctgag------gcgatg---agccaaacaaac---------------------------agtaccata---atgatg------cagagaagcaat---------ttt---aaaggagccaaaaga------attattaaatgcttcaactgtggcaaggaaggg---cacatagcaaaaaattgcagggcccctaggaaaaagggctgttggaaatgtggaaaagaaggacaccaaatgaaagactgt---------------actgaaaggcaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagagcaggccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaagtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggagtc------------gacagacag---------------------------gga------------------------acacttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggccagataaaagaggctctcttagatacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaaaggctataggtacagtattggtagggcctacgcctgtcaac---ataattggaagaaacatgttgactcagcttggatgcacactaaattttccaataagttccattgacactgtaccagtaaaactgaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacagaaatttgtgaa------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccagtatttgccataaaaaagaaggacagt------accaagtggagaaaattagtagatttcagagaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtaacagtactggatgtgggggatgcatat---ttttcagttcctttagatgaaggcttcaggaaatatactgcattcaccatacctagcataaacaatgaaacaccagggattagatatcaatataatgtgcttccacaggggtggaaaggatcaccagcaatattccaaagtagcatgacaaaaatcttagaaccttttagagcaaagaatccagaaatagtcatctaccaatatatggatgacttgtatgtaggatctgacttagaaataggacaacatagagcaaaaatagaggagttaagagaacatctattaaagtggggatttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttatgcagggattaaagtaaagcaactttgtaaactcctcaggggggccaaagcactaacagatatagtaccactaactgaagaagcagaattagagttagcagagaacagggaaattctaagagaaccagtacatggggtatattatgacccatcaaaggacttgatagctgaaatacagaaacaggggaatgaccaatggacatatcaaatttaccaagagccattcaaaaacctgaaaacagggaaatatgcaaaaatg---aggagtgcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccttggagagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaagaaacatgggagacatggtggacagactattggcaagccacatggactcctgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagctagagaaagaacccatggtaggagcagaaaccttctatgtagatggagcagctaatagggaaactaaaataggaaaagcagggtatgttactgacaaaggaagacagaaa---gttgttactctaactgaaacaacaaaccagaggactgaattacaagcaatttacctagctttgcaagattcaggatcagaag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+>C.ZA.03.03ZAPS081MB1.DQ351219
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtggct---ctggt-a---------------actagagatc-------cctcagaccctt-tttg-g-tggtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-gggctcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc-----------------------aattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagaggcgaaaaattagataaatgggaaagaattaggtta---agg------cca---gggggaaagaaaagctatatgttaaagcatctagtatgggcaagcagggagctggaaagatttgcacttaaccctggtcttttagaaacatcagaaggctgtaaacaaataatgaaacagctacaaccagct---cttaagacaggaacagaggaacttaagtcattatacaacacagta---gcaactctctattgtgtacatgaaaggatagaggtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaagtcag------------------------caaaaaacacagcaggaaaaagcg---------------------gctgacggg------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcaaaaccttcaagggcaaatggtacatcagcccctatcacctagaaccttgaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaataccatgttaaatacggtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaagaggctgcagaatgggatagattacat---ccagtacatgca---gggcctattgcaccaggccaaatg---agagagccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------agtaatcca---cct---att---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtgagaatgtatagccctgtcagcattttggacataagacaagggccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagagctgaacaagctacacaagaggtaaaaaattggatgacagacaccttgttggtccaaaatgcaaacccagattgtaagaccattttaagagcattaggaccaggggctacattggaagaaatgatgacagcatgtcagggagtgggaggacctagccataaa---gcaagagtgttggctgag------gcaatg---agccaaacgaac------------------------agtgcaaacata---atgatg------cagagaggtaat---------ttt---aaaggccctaaaaga------attgttaaatgtttcaactgtggcaaggaagga---cacatagccagaaattgcagagcccctaggaaaaagggctgttggaaatgtgggaaagaaggacaccaaatgaaagattgt---------------actgaaaggcaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttcctccagaacagaccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggagtc------------gaaggacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgaccccttgtcacaataaaagtagggggccagataaaggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ttggctttgccaggaagatggaaaccaaaaatgataggaggaattggaggctttatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaaaggctataggtacagtattagtagggcctacacctgtcaac---ataattggaagaaacatgttgactcagctcggatgtacactaaattttccaattagtcctattgaaactgtacctgtaaaactgaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacagcaatttgtgaa------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggatagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttgggaa---gtacag------tta---ggaata---------------------------ccacatccagcagggttaaaaaagaaa---aaa------tcagtgacagtgctggatgtgggggatgcatat---ttttcagttcccttagatgaaagcttcaggaaatatactgcatccaccatacctagtataaacaatgaaacaccaggaatcagatatcaatataatgtgctcccacagggatggaaaggatcaccatcaatattccaaagtagcatgacaaaaatcttagagccctttagagcaaaaaatccagaaatagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaacagggcaacatagagcaaaaatagaggagttaagaaaacatttattaagttggggacttactacaccagacaaaaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagctagtgggaaaattaaactgggccagtcagatttacccagggattaaagtaaagaaactttgtaaactccttaggggggccaaagcactaacagacatagtaccactaactgaagaagcagaattagaattagcagagaacagggaaattttaaaagaaccagtacatggagtatattatgacccatcaaaagacttaatagctgaaatacagaaacagggggatgaccaatggtcatatcaaatttaccaggaaccattcaaaaatctgaaaacagggaagtatgcaaaaatg---aggactgcccacactaatgatgta------agacagttaacagaggcagtgcaaaaaatagctttggaaagcatagtaatatggggaaag---actcccaagtttagactacccatccaaaaagaaacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatactcctcccctagtaaaattatggtaccagctggagaaagaacccatagcaggagcagaaactttctatgtagatggagcagccaatagggaaactaaaaggggaaaagcagggtatgttactggcagaggaaggcagaaa---attgtttctctaagtgaaacaacaaatcagaagactgaattacaagcaattcagctagctttgcaagattcaggaacagaag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+>C.ZA.03.03ZAPS083MB1.DQ351229
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+>C.ZA.03.03ZAPS086MB1.DQ275654
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+>C.ZA.03.03ZAPS089MB1.DQ351216
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtggct---ctggt-a---------------actagagatc-------cctcagaccctt-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------tagaaccagagga--------gttctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc-----------------------aaatttattggact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagaggcgaaaatttggatagatgggaaaaaattaggtta---agg------cca---gggggaaagaaacattatatgttaaaacacatagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacagcagaaggctgtaaacaaataatgcaacagctacaaccagct---cttcagacaggaacagaggaacttaaatcattattcaacacagta---gcaactctctactgtgtacatagaaagatagatatcagagacaccaaggaagccttagacaagatagaggaagaacagaacaaaagtcag------------------------caaaaaacacagcaggcaaaagcg---------------------gctgacgaa------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatcttcaagggcaaatggtacatcaggccatatcacctagaaccttgaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattgtcagaaggagccaccccacaagatttaaacaccatgttaaatacggtggggggacatcag---gcagccatgcaaatg---ttaaaagat---accatcaatgaagaggctgcagaatgggataggttacat---ccagtacatgcg---gggcctgttgcaccaggccaaatg---agagaaccaaggggaagcgatatagcaggaactactagtacc---cttcaggaacaaatagcatggataaca---------ggtaaccca---cct---att---ccagta---ggagaaatctataaaagatggataattctggggttaaataaaatagtgagaatgtatagccctgtcagcattttggacataaaacaagggccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagagccgaacaagctacgcaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaacccagactgtaagaccattctaagagcattaggaccaggggctacattagaggaaatgatgacagcatgtcagggagtgggaggacctggccacaaa---gcaagagtgttggctgag------gcaatg---agtcgagcaaac------------------------agtgcaaacata---atgatg------cagagaagcaat---------ttt---aaaggccctaaaaga------attgttaaatgcttcaactgtggcaaggaaggg---catatagccaaaaactgcagggcccctaggaaaaaaggctgttggaaatgtggaaaggaaggtcaccaaatgaaagattgc---------------actgagagacaggctaattttttagggaaaatttggcc---ttccaacaa------ggg---gag---gccagggaatttccttcagagcagaccagagccaacagc------------------------------------------------------cccaccagc------ggagagcttcaggtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------acaggagca------------gaaagacag---------------------------gga------------------------acccttaactgccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggtcaggtaaaagaggctctcttggacacaggagcagatgatacagtatta---gaagac---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatagttatagaaatttgtggaaaaaaggctataggtacagtgttagtagggcctacacctgtcaac---ataattgggagaaatatgttgactcaacttggatgcacactaaattttccaattagtcccattgaaactgtaccagtaaaactgaagccagggatggatggcccaaaggttaaacag---tggccattgacagaagaa---aaaataaaagcattaacagcaatttgtgaa------gaaatggagaaggaaggaaaaattacaaga---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aag------tcagtgacagtactggatgtgggggatgcatat---ttttcagttcctttagataaaagcttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccagggattagatatcaatataatgtacttccacagggatggaaagggtcaccagcaatattccagagtagcatgacaaaaatcttagagccctttagagcaagaaatccagaaatagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagggcaacacagagcaaaaatagaggagttaagagaacatttattaaggtggggatttaccacaccagacaagaaacatcaaaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacaactgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacccagggatcaaagtaaaacaactttgtaaactccttaggggggccaaagcactaacagacatagtaccactaactgaagaagcagaattagaattagcagagaacagagaaattctaaaagaaccagtacatggagtatattatgactcatcaaaagaattaatagctgaaatacagaaacaggggaatgaccaatggacatatcagatttaccaagagccattcaaaaatctgaaaacaggaaagtatgcaaaaatg---agaactgcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccttggaaagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaagagacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtgaaattatggtaccagctggagaaagaacccatagtaggagcagaaactttctatgtagatggggcagctaatagggaaactaaattaggaaaagcaggatatgttactgacagaggaaggcagaaa---attgtttctctaactgaaacaacaaatcagaagactgaattgtaagcaattcagctagctttgcaagattcaggatcagaag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+>C.ZA.03.03ZAPS091MB1.DQ275645
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+>C.ZA.03.03ZAPS094MB1.DQ396377
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+>C.ZA.03.03ZAPS095MB1.DQ275652
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccctt-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcacttggcaagaggc-------------ga-g-ag--gggc-----ggctggtgagtacgcc----------------------aaatttcatttgact----------agcgga-gg---------ctagg-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggggggaaattagataaatgggaaaaaattaggtta---agg------cca---gggggaaagaaaaagtatatgctaaaacatttagtatgggcaagcagggagctggaaagatttgcacttgaccctggccttttagaaacatcagaaggctgtagacaaataatgaaacagctacaaccagct---cttcagacaggaacagaggaacttaaatcattattcaacacagta---gcaactctctattgtgtacatgaaggcatagatgtacgagacaccaaagaagccttagacaaaatagaggaagaacaaaataaaagtcag------------------------caaaaaacacagcaggcaaaagtg---------------------gctgacgga------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtgcatcaagccatatcacctagaaccttaaatgcatgggtaaaagtgatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagctaccccacaagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcagatg---ttaaaagat---accatcaatgaggaggctgcagaatgggacagattacat---ccagtacatgca---gggcctattgcaccaggtcaattg---agggagcctaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------aataatcca---cct---gtc---ccagtg---ggagacatctataaaagatggataattctggggttaaataagatagtaagaatgtatagccctgtcagcattttggacataagacaagggccaaaggaaccttttagagactatgtagaccggttctttaaaactttgagagccgaacaagctacacaagatgtaaaaaattggatgacagataccttgttggtccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccaggggctacattagaagaaatgatgacagcatgtcaaggagtgggaggacctagccacaaa---gcaagagtgttagctgag------gcaatg---agccaaacaaac---------------------------agtaacata---atgatg------cagagaagcaat---------ttt---aaaggacctaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccagaaattgcagggcccctagaaaaaagggctgttggaaatgtggaaaagaaggacacccaatgaaagactgt---------------actgagaggcaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagaacagaccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---agc---aac---ccccgc------------------------------tccgaa---------------gcaggagtc------------gaaagacag---------------------------gga------------------------acccttaatttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggccagataaaggaagctctcttagacacaggagcagatgatacagtatta---gaagat---ataagtttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaaaggctataggtacagtattagtaggacctacacctgtcaac---ataattggaaggaatatgttgactcagcttgggtgcacactaaattttccaattagtcccattgaaactgtaccagtaaaactgaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacagcaatttgtgaa------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataatactccaatatttgctataaaaaagaaggatagt------actaaatggaggaaattagtagatttcagggaacttaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtgacagtattggatgtgggggatgcatat---ttttcagttcctttagatgaaagcttcaggaaatatactgcattcaccatacctagtaaaaataatgaaacaccagggattagatatcaatataatgtgcttccacagggatggaagggatcaccagcaatattccaaagtagcatgacaaaaatcttagagccctttagagcaaaaaatccagatatagtcatctatcaatatatggatgacttatatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaggagttaagacaacatctgttaaagtggggattcaccacaccagataagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaaattagtgggaaaattaaactgggcaagtcagatttacccagggattaaagtaaggcaactttgtaaactccttaggggggccaaagcgctaacagacatagtaccactgactgaagaagcagaattagaattagcagagaacagggaaattctaaaagaaccagtacatggagtatattatgacccatcaaaagatttgatagctgaaatacagaagcagggaaatgaccaatggacatatcaaatttaccaagaaccattcaaaaatctgaaaacaggaaagtatgcaaaaatg---aggacagcccacactaatgatgta------aaacagttaacagaggcaatacaaaaaatagccatggaaagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaagaaacatgggagacatggtggacagactattggcaagccacctggatccctgaatgggagtttgttaatacccctcccctagtaaaattatggtaccagccggagaaagaacccatagcagaagcagaaactttctatgtagatggggcagctaataaggaaactagaacaggaaaagcagggtatgttactgatagaggaagacagaaa---gttgtgactataactgaaacaacaaatcagaagactgaattacaagccattcagctggctttgcaagattcaggatcaaaag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+>C.ZA.03.03ZAPS097MB1.DQ351230
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+>C.ZA.03.03ZAPS099MB1.DQ275655
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+>C.ZA.03.03ZAPS103MB2.DQ275656
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+>C.ZA.03.03ZAPS105MB2.DQ445632
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+>C.ZA.03.03ZAPS108MB1.DQ396378
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+>C.ZA.03.03ZAPS112MB2.DQ396386
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+>C.ZA.03.03ZAPS116MB1.DQ445635
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+>C.ZA.03.03ZAPS122MB1.DQ396370
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+>C.ZA.03.03ZAPS124MB1.DQ369976
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+>C.ZA.03.03ZAPS125MB1.DQ396390
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtggct---ctggt-a---------------actagagatc-------cctcagaccaag-ttgg-t-tcgtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------tgagaccagagaa--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--gggc-----ggctggtgagtacgcc---------------------aaattttattttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagagggggaaagttagatgcatgggaaagaattaggtta---agg------cca---gggggaaagaaacattatatgctaaaacacttagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttggagacatcagaaggctgtaaacaaataataaaacagctacacccagct---cttcagacaggatcagaggaacttaagtcattatacaacacagta---gcaactctctattgtgtacatgaaaagatagaagtacgagacaccaaggaagccttagacaagatagaggaagaacaacagagatgtcag------------------------caaaaaacacagcaggcaaaagcg---------------------gctgacggg------------------------------aaa------------------------gtcagtcaaaattaccctata------------gtgcagaacctccaagggcaaatggtacatcaggccatatcacctagaactttgaatgcatgggtaaaagtgatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagacctaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcagatg---ttaaaagat---accatcaatgaggaggctgcagaatgggataggttacat---ccagtacatgca---gggcctcctgcaccaggccaaatg---agggaacctaggggaagtgacatagcgggaactactagtacc---cttcaggaacaaatagcatggatgaca---------ggaaaccca---cct---gtc---ccagtg---ggagacatctataaaaggtggataattctggggttaaataaaatagtaagaatgtacagccctgtcagcattttggacataaaacaggggccaaaagaaccctttagagactatgtagaccgattctttaaagttttaagggctgaacaagctacacaagatgtaaaaaattggatgacagaaaccttgctggtccaaaatgcgaacccagattgtaagaccattctaaaggcattgggaccagcggcttcattagaagaaatgatgacagcatgtcagggagtgggaggacctggtcacaaa---gcaagagtgttggctgag------gcaatg---agccaagcaaac---------------------------aataacata---atgatg------cagagaagcaat---------ttt---aaaggacctagaaga------attgttaaatgcttcaactgtggcaaggaaggg---cacatagccaaaaattgcagggcccctaggaaaaaaggctgttggaaatgtggaaaagaaggacaccaaatgaaagactgt---------------actgagagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---gag---gccagggaatttcctccagagcaggccagagccgtcagc------------------------------------------------------tccaccagc------agagagcttcaggtt------------cgagga---gac---agc---ccccac------------------------------tccgaa---------------gcaggagtc------------gaaagacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgaccccttgtctcagtaagagtagggggacaaataaaggaggctctattagacacaggagcagatgatacagtatta---gaagag---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacttatagaaatctgtggaaaaaaggctataggttcagtattagtaggacctacacctgtcaac---ataattggaagaaatatgttgactcagcttggatgcacactaaattttccaattagccccattaaaactgtaccagtaaaattaaagccaggaatggacggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacaggaatttgtgag------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgctataaaaaagaaagacagt------actaagtggaggaaattagtagatttcagggagctcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccccacccagcaggattaaaaaagaaa---aaa------tcagtgacagtactagacgtgggggatgcatat---ttttcagtccctttagatgagagcttcagaaaatatactgcatttaccatacctggtgtaaacaatgaaacaccaggaattagagatcaatataatgtgctcccacagggatggaagggatcaccagcaatattccagtatagcatgacgaaaatcttagagccctttagagcaaaaaatccagaaatagtcatctatcaatatatggacgatttatatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaagagctaagagaacatctattaaagtggggattcaccacaccagataagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaagtggacagtacagcctataaagctgccagaa---aaagat---agctggactgtcaatgatatacagaagttagtaggaaaattaaactgggcaagtcagatttacccagggattagagtaaagaacctttgtaaactccttaggggggccaaagcactaacagacataataccattaactgaagaagcagagttagaattggcagagaacagggaaattctaaaagaaccagtacatggagtatattatgacccatcaaaagagttgatagctgaaatacagaaacaggggcaggatcaatggacatatcaaatttatcaagaaccattcaaaaatctgaaaacagggaagtatgcaaaaagg---aggacggcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccatggaaagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaggaaacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagctggagaaagagcccatggcagaagtagaaactttctatgtagatggagcagctaatagggaaactaaaataggaaaagcagggtatgttactgacagaggaaggcagaaa---gttgttactctaactgaaccaacaaatcagaaggctgaattacaagcaattcagctagctttgcaagattcaggaccagaag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+>C.ZA.03.03ZAPS128MB1.DQ275643
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+>C.ZA.03.03ZAPS130MB1.DQ275658
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+>C.ZA.03.03ZAPS131MB1.DQ396380
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+>C.ZA.03.03ZAPS133MB1.DQ275646
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+>C.ZA.03.03ZAPS136MB1.DQ351231
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+>C.ZA.03.03ZAPS143MB1.DQ396391
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+>C.ZA.03.03ZAPS151MB1.DQ396392
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+>C.ZA.03.03ZAPS152MB1.DQ396399
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------gctagagatc-------cctcagatcctt-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cctgaacagggac------------------ccgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc-----------------------aattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattacgaggcgaaaaattagatagatgggaaagaattaggttg---agg------cca---gggggaagcaaacgttatatgttaaaacacatagtatgggcaagcagggagctggaaagattcgcacttaaccctggcctcttagaaacatcagatggctgtaaacaaataataagccagttacaaccagct---cttaagacagggacagaggaacttaaatcattatacaacacagta---gcaactctctattgtgtacataaaaacatagatgtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaagtcag------------------------caaaaaacacagcaggcaaaagag---------------------gctgacgga------------------------------aaa------------------------gtcagtcaaaattatcctata------------gttcagaatcttcaagggcaaatggtacaccaatctctatcacctagaactttgaatgcatgggtaaaagtgatagaggagaaa------gccttcagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatctaaacaccatgttaaatacagtggggggacatcag---gcagccatgcaaatg---ttaaaagac---accatcaatgaggaggctgcagaatgggataggacacat---ccagtacatgca---gggcctgttgcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggagcaaatagcatggatgaca---------ggtaaccca---ccc---gtt---ccagta---ggagaaatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagcccagtcagcattttggacataagacaagggccaaaggaaccctttagggactatgtagatcggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagaaaccttgttggtccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccaggggccacattagaagaaatgatgacggcatgtcagggagtgggaggacctagccacaaa---gcaagagtattggctgag------gcaatg---agtcaagcaaac------------------------agtacaaaaata---atgata------cagaatagcaat---------ttt---aaaggccctagaaga------attattaaatgtttcaactgtggcaaggaaggg---cacctagccagaaattgcagaacccctaggaaaaaaggctgttggaaatgtggaagggaaggacaccaaatgaaagactgt---------------actgaaaggcaggctaattttttagggaaaatttggcc---ttcccacagcaa---ggg---gag---gccagggaattttcttcagaacaggccagagccaacagc---------------------------------cccaccagcagagccaacagccccaccagc------agagagcttcaggtt------------cgagga---gac---aac---cccagc------------------------------tccgaa---------------gcaggagat------------gaaagacag---------------------------gga------------------------acctttaacttccctcaaatcactctttggcaacgacccctggtctcaataaaaatagcgggccagataaaggaggctctcttagacacaggggcagatgatacagtgtta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgatagggggaattggaggttatatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaaaggctataggtacagtattagtagggcctacacctatcaat---ataattggaagaaatatgttgactcagcttggatgcacactaaattttccaataagtcctattgagactgtaccagtaaaactgaagccaggaatggatggcccgaagattaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagcaatttgtgag------gacatggaaaaggaaggaaaaatttcaaaa---attgggcct---gaaaacccatataacactccaatatttgccataaaaaagaaagacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttgtgag---gttcaa------ttg---ggaata---------------------------ccacacccagcagggttaaaaaggaag---aaa------tcagtgacagtactggacgtgggggatgcatat---ttttcaattcctttagatgaaggcttcaggaaatatactgcattcaccatacctagtataaataatgaaacaccagggactagataccaatataatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaagaatcttagaaccctttagagcaaaaaatccagaaatagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaggagttaagagaacatctattaaagtggggacttactacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagag---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttactcagggattaaagtaaggcaactttgtaaactccttaggggggccaaagcactaacagacatagtaccactaactgaagaagcagaattagaattggcagagaacagggaaattctaaaagaaccagtacatggggtatattatgacccatcaaaagacttgatagctgaaatacagaaacaagggcagggccaatggacatatcaaatttaccaagaaccattcaagaacctaaaaacagggaagtatgcaaaaatg---aggactacccacactaatgatgta------aaacagttagcagaggcagtgcaaaaaatagccttggaaagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaagaaacatgggaaatatggtggacagattattggcaggccacctggattcctgagtgggagtttgttagtacccctcccctagtaaaattatggtaccagctggagaaagaacccatagcaggagcagaaactttctatgtagatggagcagctaataggaaaactaaaatgggaaaagcagggtatgttactgacagaggaaggcaggaa---attgttcctctaactgaaacaacaaatcagaaaactgaattacaagcaattcatctagctttgcaagattcaggatcagaag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+>C.ZA.03.03ZASK005B2.DQ011175
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccagt-tttg-g-gagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------cagaaagcgaaag------------------------------------------taagaccagagaa--------gaactctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------gagg-gg--cggc-----gactggtgagtacgcc----------------------gaattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattacgagggggaaaattagatgcatgggaaagaattaggcta---agg------cca---gggggaaagaaacattatatgctaaaacacttagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttctagagacatcagaaggctgtaaacaaatactaaaacagctacacccagct---cttcagacaggaacagaggaacttaaatcattatacaacacagta---gcaactctctattgtgtacatgaaaagatagaggtacgagacaccaaagaagccttagataagatagaggaagaacaaaacaaaattcag------------------------caaaaaatgcagcagacaaaaaag---------------------actgatgaa------------------------------aaa------------------------gccagtcaaaattaccctata------------gtgcagaatcttcaagggcaaatggtacaccaggcaatatcacctagaaccttgaatgcatgggtaaaagtgatagaggagaag------gcttttagcccagaagtaatacccatgtttacggcactatcagaaggagcctccccacaagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcagatg---ttaaaagat---accatcaatgaggaggctgcagaatgggacagaatgcat---ccagtacatgca---gggcctattgcaccaggccaaatg---agggagcctagggggagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------agtaaccca---cct---gtc---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggatataagacaagggccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttgctccaaaatgcaaacccagattgtaagaccattttaaaggcattaggaccaggggcttcattagaagaaatgatgacagcatgtcaaggagtggggggacctagccacaaa---gcaagagtgttggctgag------gcaatg---agccaaacaaat---------------------------aatagcata---atgatg------cagagaagcaat---------ttt---aagggatctaagaga------attgttaagtgtttcaactgtggcaaggaaggg---cacatagccagaaactgcagggcccctaggaaaaaaggctgctggaaatgtgggaaagaaggacaccaaatgaaagactgt---------------actgagaggcaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---gag---gccagggaacttcattcagagcaggccagagccgacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggagtc------------gaaggacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggccagataaaggaagctctattagacacaggagcagatgatacagtatta---gaagag---ataaatttgccaggaaaatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---ggtcaaatagttatagaaatttgtggaaaaagggctataggtacagtattagtaggacctacacctgtcaac---ataattggaagaaatatgttgactcagttaggatgcacactaaattctccaattagtcccattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagcaatttgtgaa------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagt------actaagtggaggaaattagtagatttcagggaactcaataaaaggactcaagatttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcaggattaaaaaagaaa---aaa------tcagtgacagtactagatgtgggggatgcctat---ttttcagttcctttagatgaaggcttcaggaaatatactgcatttaccatacctagtataaacaatgaaacaccagggattagatatcagtataatgtgcttccacagggatggaaaggatcaccagcaatatttcagtctagcatgacaagaatcttagagccctttagggcacaaaatccagaaatggtcatctatcaatatatggatgacttatatgtaggatctgacttagaaataggacaacatagagcaaaaatagaggagttaagagcacatctgttaaggtgggggttcaccacaccagataagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctataaagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggccagtcagatttacccagggattaaagtaaggcaactttgtaaactccttagggggaccaaagcactaacagacatagtaccactaactgcagaagcagaattagaattggcagagaacagagaaattctaaaagaaccagtacatggagtatattatgatccatcaaaagacttggtagctgaaatacagaaacagggggaggatcaatggacatatcagatttaccaagaaccatttaaaaatctgaaaacagggaaatatgcaaaaagg---aagacagcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagcagtggaaagcatagtaatatggggaaag---actcctaaatttagactgcccatccaaaaagaaacatgggagacatggtggacagattattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccctagtaaaattatggtaccagctagagaaagaacccatagcaggagcagaaactttctatgtagatggagcagctaatagggaaactaaaatgggaaaagcagggtatgttacagacagaggacgacagaaa---gttgttactctaaatgaaacaacaaatcagaagactgaattacaagcaattcagctagctttacaagattcaggattagaag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+>C.ZA.03.03ZASK006B2.AY878056
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccctt-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagaa--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc----------------------aaattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggggagaatttggatagatgggaaaaaattaggtta---agg------cca---gggggaaagaaacaatataggttaaaacatttagtatgggcaagcagggagctggaaagattcgcacttaaccctggccttttagaaacatcagagggctgtaaacaaatactggcacagctacaaccagct---cttcagacaggaacagaggaaattaaatcactatacaacacagta---gcaactctctattgtgtacataaaaagatagatgtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaagtcag------------------------caaaaaacacaacaggcaaaaacg---------------------gctgacgga------------------------------aag------------------------gtcagtcaaaattatcctata------------gtacagaatctccaagggcaaatggtacatcaagccatatcacctagaaccttgaacgcatgggtaaaagtaatagaagagaag------ggctttaatccagaagtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacgatagggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaggaggctgcagaatgggatagattacat---ccagtacatgca---gggcctgttgcaccaggccaaatg---agggaaccaaggggaagcgacatagcaggatctactagtacc---cttcaggaacaagtagcatggattaca---------ggtaatcca---gct---atc---ccagtg---ggagaaatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaagggccaaaggaaccctttagagactatgtaggtcggttctttaaagctttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaacccagattgtaagaccattttgaaatcattaggaacgggggctacattagaagaaatgatgacagcatgccagggagtgggaggacctagccacaaa---gcaagagtgttggctgag------gcaatg---agccaggcaaac------------------------agtacaaacata---atgatg------cagagaagcaat---------ttt---aaaggctctagaaga------gttgttaaatgtttcaactgtggcaaggagggg---cacatagccaaaaattgcagggcccctagaaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagactgt---------------actgagagacaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccaggaaattttttgcagaacagaccagagccaacagc------------------cccaccagcagagagcttcagaccagagccaacagccccaccagc------agagagcttcaggtt------------cgagga---gac---acc---ccccgc------------------------------tccgaa---------------gcaggagcc------------gaaagacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgacccctggtctcaataaaagtaggaggccaaataaaagaggctctcttagatacaggagcagatgatacagtattg---gaagaa---ataaatttgccaggaaaatggaaaccaagaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacctatagaaatttgtggacaaaaggcaataggtacagtattagtagggcctacacctgtcaac---ataattggaagaaatctgttgactcagcttggatgcacgctaaattttccaattagtcccattgaaactgtaccagtacaactgaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacagaaatttgtgaa------gaaatggaaagggagggaaaaattacaaaa---attgggcct---gaaaatccatataacactccagtatttgccatcaaaaagaaggatggt------aataaatggagaaaattagtagatttcagggaactcaataaaaggacccaagacttctgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtgacagtactggatgtgggagatgcatat---ttttcagttcccttatatgaaggcttcaggaaatatactgcattcaccatacctagtataaacaatgaagcaccagggattagatatcaatataatgtgcttccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaagatcttagagccctttagagcacaaaatccagaaatagtcatctatcaatatatggatgatttgtatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaggagttaagagaacatctattaaagtggggatttaccacaccagacaagaaacatcagaaagaacccccatttctctggatgggatatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttatgcagggattaaagtaaggcaactttgtaaactccttaggggggtcaaggcactaacagacatagtaccactaactgaagaagcagaattagaattggcagagaacagggaaattctaaaggaaccagtacatggagtatattatgacccatcaaaagacctaatagctgaaatacagaaacagggggatgaccaatggacatatcaaatttaccaagaaccattcaagaatctgaaaacaggaaagtatgcaaaaatg---aggaatgcacacattaatgatgta------aaacagctaacagaggcagtgcaaaaaatagcattggaaagcatagtgatatggggaaag---actcctaaatttagactacccatccaaaaagaaacatgggaggtatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagctggagaaagaacccatagcaggagcagaaactttctatgtagatggagcagctaatagggaaactaaaaaaggaaaagcagggtatgttactgacaaaggaaggcagaaa---attgtttctctaagtgaaacaacaaaccagaagactgaattacaagcaattcaactagctttgcaagattcaggaccagaag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+>C.ZA.03.03ZASK011B2.AY901965
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccaac-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----gactggtgagtacgcc----------------------aaattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagaggcgaaaaattagataaatgggaaaaaattaggtta---agg------cca---gggggaaagaaaaaatatatgataaaacacatagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacagcagaaggctgtaagcaaatactgcaacagctacaaccagct---cttaagacaggaacagaggaacttagatcattatataacacagta---gcaactctctattgtgtacatgcaaggatagaggtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaagtcag---------------------caaaaaacacagcaggcaaaaccggct------------------ccggctgatgga------------------------------aag------------------------atcagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtacatcaagccatatcacctagaaccttgaatgcatgggtaaaagtaatagaggaaaaa------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacggtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgacgaggctgcagaatgggatagattacat---ccagtacatgca---gggcctattgcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtaac---cttcaggaacaaatagcatggatgaca---------ggtaaccca---cct---gtt---cctgtg---ggagaaatctataaaagatggataattctggggttaaataaaatagtgagaatgtatagccctgtcagcattttggacataagacaaggaccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagagctgaacaagcttcacaagatgtaaaaaattggatgacagataccttgttggtccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccaggggctacattagaagaaatgatgacagcatgtcagggagtggggggacctggccacaaa---gcaagagtgttggctgag------gcgatg---agccaagcaaac------------------------aatataaacata---atgatg------cagagaaacaac---------ttt---aaaggctctaacaga------attgttaaatgttttaactgtggcaaggaaggg---cacatagccagaaattgcagagctcctaggaaaaaaggctgttggaaatgtggaaaggaaggacaccaaatgaaagactgt---------------actgaaaggcaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagaacagaccagagccaacagc------------------------------------cccaccagagccaacagccccaccagc------agagagcttcaggtt------------cgggga---gac---aac---ccctgc------------------------------tccgaa---------------gcaggagca------------gaaagacag---------------------------gga------------------------acctttaatttccctcaaatcactctttggcagcgaccccttgtcacaataaaagtagggggccaggtaaaggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaacttgccagggaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacccatagaaatttgtgggaaaaaggctataggtacagtattagtagggcctacacctgtcaac---ataattggaagaaacatgttgactcaacttggatgcacactaaattttccaattagtcctattgaaactgtaccagtaaaactgaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagcaatttgtgaa------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataatactccaatatttgccataaaaaagaaggatagt------actaaatggagaaagttagtagatttcagggaactcaataaaagaactcaggatttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtgacagtactagatgtgggggatgcatat---ttttcagttcctttagatgaaagcttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccagggattagatatcaatataatgtgcttccacaaggatggaaggggtcaccagcaatattccagtctagcatgacaaaaatcttagagccctttagagcacaaaatccagaaatagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaagagttaagagaacatctattgaagtggggatttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtgcagcctatacagctaccagaa---aaagat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttaccgagggattaaagtaaggcaactttgtaaactccttaggggggccaaagcactaacagacatagtaccactaactgaagaagcagaattagaattggcagagaacagggaaattctaaaagagccagtacatggagtatattatgacccatcaaaagacttgatagctgaaatacagaaacaggggggtgaccaatggacatatcaaatttaccaagagccattcaaaaatctgaaggcaggaaagtatgcaaaaatg---aggactgcccacactaatgatgta------aagcagttaacagaggcagtgcaaaaaatagcccaggaaagcatagtgatatggggaaag---actcctaagtttagactacccatccaaaaagaaacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagctggaaaaagaacccatagcaggagcagaaactttctatgtagatggagcagctagtagggaaactaaaataggaaaagcagggtatgtcactgacaaaggaaggcagaaa---attgtcactctaaatgaaacaacaaatcagaagactgaattacaagcaattcagctagctttgcaagactcaggatcagaag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+>C.ZA.03.03ZASK026B2.DQ011165
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+>C.ZA.03.03ZASK036B1.AY901966
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+>C.ZA.03.03ZASK058B2.AY901967
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccaat-tgtg-t-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------gcgaaagcgaaag------------------------------------------taagaccagagaa--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaggaggc-------------ga-g-gg--gggc-----gactggtgagtacgcc----------------------aatttttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagaggcgaaaaattagatcattgggaaagaattaagctg---agg------cca---gggggaaagaaacattatatgctaaaacacatagtatgggcaagcagagagctggaaagatttgcacttaaccctggccttttagaaacagcagaaggctgtaaacaaataataagccagctacaaccagct---cttaagacaggaacagaagaacttaaatcattatacaacacagta---gcaactctctattgtgtacataaaaagatagaaataagagacaccaaggaagccttagacaagatagaagaagaacaaaacaaaagtcaa------------------------caaaaaacacagcaggcagcagcg---------------------gctgacgga------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatctgcaagggcaaatggtacatcagcccatatcacctagaaccttgaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaggaggctgcagaatgggatagattacat---ccagtacatgca---gggcctgttgcaccaggccaaatg---agagagccaaggggaagcgacatagcaggaactactagtacc---cttcaggatcaaatagcatggataaca---------ggtaaccca---cct---att---ccagtg---ggagaaatttataaaagatggataattctggggctaaataaaatagtgagaatgtatagccctgtcagcattttggacataagacaagggccaaaggaaccctttagagactatgtagatcggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcaaacccagattgtaagaccattttaagagcattaggaccaggggctacattagaagaaatgatgacagcatgtcaaggagtgggaggacctggccacaaa---gcaagagtattggctgag------gcaatg---agccaagtaaacaatgga---------------aacaatggaaacatc---atgatg------cagagaggcaat---------ttt---aaaggccctaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccaaaaactgcagggcccctaggaaaaaaggctgttggaaatgtggaaaggaaggtcaccaaatgaaagactgc---------------attgaaagacaggctaattttttagggagattctggcc---ttcccacaa------ggg---gag---gccagggaacttccttcagagcagaccagagccatcagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggagcc------------gaaggacag---------------------------gga------------------------acctttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggccaggtaaaggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacccatagaaatttgtggaaaaaaggctataggtacagtattggtagggcctacacctgtcaac---ataattggaagaaatctgttgactcagcttggatgcacactaaattttccaattagtcccattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacagaaatttgtgaa------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccagtatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagacttcagggaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaagaaagaaa---aaa------tcagtgacagtactagatgtgggggatgcatat---ttttcagttcctttagatgaagacttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccagggattagatatcaatataatgtgctcccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaaaatcttagagccctttagagcaaacaatccagaaatagtcatctatcaatatatggatgacttgtatataggatctgacttagaaatagggcaacatagagcaaaaatagaagagttaagagaacatctattgaagtggggatttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggac---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacccaggaattaaagtaaagcaactttgtaaactcattaggggggttaaagcactaacagacatagtaccactaactgaagaggcagaattagaattggcagagaacagggaaattttaaaagaaccagtacatggggtatattatgacccatcaaaagacttaatagctgaaatacagaaacaggggcagggccaatggacatatcaaatttaccaagaaccattcaagaatctgaaaacagggaagtatgcaaaaatg---agaactgcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccatggaagctgtagtaatatggggaaag---actcctaaatttagactacctatacaaaaggaaacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaacacccctcccctagtaaaattatggtaccagttggagaaagaacccatagcagaagcagaaactttctatgtagatggagcagctaatagggaaactaaaataggaaaagcaggatatgttactgacaggggaaggcaaaaa---attatctctctgactgaaacaacaaatcagaaaactgaattacaagcaattcagctagctttgcaagattcaggatcagaag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+>C.ZA.03.03ZASK066B1.AY901969
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagac-cct-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------gcgaaagcgaaag------------------------------------------taagaccagagaa--------gatctctcgacgca-gggctcggcttgct---gaagtgcactcggcaagaggc-------------ga-gagg--cggc-----ggctggtgagtacgcc-----------------------aattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagaggcgaaaaattagatacatgggaaaagattaggtta---agg------cca---ggagggaagaaacattatatgctaaaacacatagtatgggcaagcagggagctggaaagatttgcactcaaccctggccttttagaaacatcagaaggctgtaagcagatattgcaacagctacaaccagct---cttcagacaggaacagaggaacttaaatcattatacaacacagta---gcaactctctattgtgtacacaaaaggatagatgtaagagacaccaaggaagccttagacaaaatagaggaagaacaaaacaaaagccag------------------------caaaaaacacagcaggcaaaagcg---------------------gctgccgag------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatctacaaggacaaatggtacaccaggctatatcacctagaactttgaatgcatgggtaaaagtgatagaggaaaag------gctttcagcccagaggtaatacccatgtttacagcattatcagaaggagccgccccacaagatctaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagac---accatcaatgaggaggctgcagaatgggatagggtacat---ccagtacctgca---gggcctattgcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtaac---cttcaggaacaaatagcatggatgaca---------agtaaccca---cct---gtt---ccagtg---ggagaaatctataaaagatggataattctggggttaaataaaatagtgagaatgtatagccctgttagcattttggacataagacaagggccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagagccgaacaagctacacaagatgtaaaaaattggatgacagaaaccttgttggtccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccaggggctacattagaagaaatgatgacagcatgtcagggagtgggaggacctagccacaaa---gcaagggttttggctgag------gcaatg---agccaagcaaac------------------------aatccacacata---atgatg------cagaagggcaat---------ttt---aaaagc---agaaga------gttgttaaatgtttcaactgtggcaaggaagga---cacatagcaagaaattgcagggcccctaggaaaaagggctgttggaaatgtgggcaagaaggacaccaaatgaaagactgt---------------actgagagacaggctaattttttagggaaaatttggcc---ttcccgcaa------ggg---gag---gccagggaatttccttcagagcagaccagagccaacagc------------------------------------------------------cccaccaat------ggagagcttcaggtt------------cgagga---aac---aac---tcccgc------------------------------tccgaa---------------gcaggagcc------------gaaagacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggtcaggtaagggaagctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatagctatagaaatttgtgggaaaaaggctataggtacagtattaatagggcctacacctgtcaac---ataattggaagaaacttgttgactcagcttggatgcacactaaattttccaattagccccattgaaactgtaccagtaaaattaaagacaggaatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattgacagcaatttgtgat------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttgaaaaagaaa---aag------tcagtgacagtactggatgtgggggatgcatat---ttttcagtgcctttagatgaaagcttcaggaaatatactgcattcaccacacctagtataaacaatgaaacaccagggattagatatcaatataatgtgcttccacagggatggaaaggatcaccagcaatatttcaaagtagcatgacaaggatcctagagccctttagagcagaaaatccagaaatagtcatctatcaatatatggatgacttatatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaggagttaagagaacatctattaaggtggggatttaccacaccagacaagaagcatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaagat---agctggactgtcaatgacatacagaagttagtgggaaaattaaactgggcaagtcagatttacccagggattaaagtaagacaactttgtaaactccttaggggggccaaagcgctaacagacatagtaccactaactgcagaagcagaattagaattagcagagaacagggaaattctaaaagaaccagtacatggagcatattatgacccatcgaaagacttaatagcagaaatacaaaaacaaggggatgatcaatggacatatcaaatttatcaagaaccattcaaaaatctgaaaacaggaaagtatgcaaaaatg---aggactgcccacactaatgatgta------aaacagttaacagcggcagtgcaaaaaatagcccaggaatgcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaggaaacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagctggagaaagaacccatagcaggagtagaaactttctatgtagatggagcagctaatagggaaactaaaatgggaaaagcagggtacgttactgacaggggaaggcaaaaa---attgtttctctaactgaaacaacaaatcagaagactgagttacaagcaattcagctagctttgcaagattcaggatcagaag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+>C.ZA.03.03ZASK072B1.DQ093593
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagaggtc-------cctcagaccctt-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagtgaagg------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--gggc-----gactggtgagtacgcc----------------------aatttttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaaggggcgaaaaattagataaatgggaaaaaattaggtta---agg------cca---gggggaaagaaacattatatgttaaaacacataatatgggcaagccaggagctggaaagatttgcactgaaccctggccttttagaaacatcagaaggctgtagacaaataataaagcagctacaaccagct---cttcagacaggaacagaggaacttaaatcattatttaacacagta---gcaactctctattgtgtacatgaaggcatagaggtacgagacaccaaggaagccttagacaagatagaggaagaacaaaaacgttgtcag------------------------caaaaaacacagcaggcaaaagcg---------------------gctgacgga------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtacatcaagccctatcacctagaaccttgaatgcatgggttaaagtaatagaggagaag------gcttttagcccagagataatacccatgtttacagcattatcagaaggagccaccccgcaagatttaaacaccatgttaaatacggtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaagaggctgcagaatgggatagaatacat---ccagtacatgca---gggcctgttgcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactaccagtaac---cttcaggaacaaatagcatggatgaca---------agtaaccca---cct---att---ccagtg---ggagatatctataaaagatggataattctggggttaaataaaatagtgagaatgtatagccctgtcagcattttggacataaaacaagggccaaaggaaccctttagagactatgtagatcggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaacccagattgtaagaccattttaagagcactaggaccaggggctacattagaagaaatgatgacagcatgtcagggagtgggaggacctggccacaaa---gcaagagtgttggccgag------gcaatg---agccacgtaaac------------------------aatgcaaatgta---atgatg------cagagaagcaat---------ttt---aaaggccctagaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccagaaactgcagggcccctaggaaaaaaggctgttggaaatgtggaaaggaaggacaccaaatgaaagactgt---------------actgagaggcaggccaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagagcaggccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gat---agc---ccccgc------------------------------gccgaa---------------gcaggagcc------------gaaggacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggtcaggtaaaagaggctctcttagacacaggagcagatgatacagtatta---gaagac---ataaatttgccaggaaaatggaaaccaagaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacctatagaaatttgtggaaaaaaggctataggtacagtattagtaggacccacacctgtcaac---ataattggaagaaatatgttgactcagcttgggtgcacactaaattttccaattagccccattgaaactgtaccagcaaaattaaaaccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacagaaatttgtgaa------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaacttaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccggcagggttaaaaaagagc---aaa------tcagtgacagtgctggatgtgggggatgcatat---ttttcagttcctttagatgaaggcttcaggaagtatactgcattcaccatacctagtataaacaatgaaacaccaggaataagatatcaatataatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatcttagagccctttagagcaaaaaatccagaaatagtcatctaccaatatatggatgacttatatgtagcatctgacttagaaatagggcaacatagagcaaaaatagaagagttaagagtacatctattaaagtggggattcaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgataaatggacagtacagcctatacagctgccagaa---aaagat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcaaatttacccagggattaaggtaaagcaactttgtaaactccttaggggagccaaagcactaacagatatagtaccactaactgaagaagcagaattagaattggcagagaacagagaaattctaaaagaaccagtacatggagtatattatgacccatcaaaagacttaatagctgaaatacagaaacagggagatgaccaatggacatatcagatttaccaagaaccattcaaaaatctgaaaacagggaagtatgcaaaaaag---agaacggcccacactaatgatgta------agacagttaacaggggcagtgcaaaaaatagccatggaaagcatagtaatatggggaagg---actcctaaatttagactacccatccaaaaggaaacatgggatatatggtggacagactattggcaagccacctggattccagagtgggagtttgttaatactcctcccctagtaaaattatggtaccagctggagaaagaacccatagcaggagtagaaactttctatgtagatggagcagctaatagggacactaaaatgggaaaagcagggtatgttactgatagaggaaggcagaaa---gttgttaccataaatgaaacaacaaatcagaagactgaattacaagcaattcagctagctttgcaagattcaggaccagaag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+>C.ZA.03.03ZASK073B1.AY901970
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcaga-ccat-tttg-g-tagcgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagaa--------gatctctcgacgca-ggactcggcttgct--gaaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc-----------------------aattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggcggaaaattagataaatgggaaaaaattaggtta---agg------cca---ggggggaagaaacgctataggctaaaacacctagtatgggcaagcagggagctggaacgattcgcacttaaccctggccttttagagacatcagaaggctgtaaacaaataatgatacagctacaaccagct---cttcaaacaggaacagaggaacttaggtcattattcaacacaata---gcaactctctattgtgtacatgcaagcatagaggtacgagacaccaaggaagccttagacaagatagaagaagagcagagcaaaagtcag---------caaaaacaaagtcagcaaaaaacacagcaggcaaaagag---------------------gctgacggg------------------------------aag------------------------attagtcaaaattatcctata------------gtgcagaatcttcaagggcaaatggtacaccaagccatatcacctagaactttgaatgcatgggtaaaagtaatagaggagagg------gcttttagcccagaggtaatacccatgtttacagcattatcagagggagccaccccacaagacttaaacaccatgttaaatacagtggggggacatcag---gcagccatgcaaatg---ttaaaagat---accattaatgaggaggctgcagaatgggacagaatacat---ccagtacatgca---gggcctattgcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacagatagcatggatgaca---------agcaaccca---ctt---gtc---ccagtg---ggagaaatctataaaagatggataattctggggctaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaaggaccaaaggagccttttagagattatgtagaccggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaacccagattgtaagatcattttaagaggattaggaccaggggctacattagaagaaatgatgacagcatgtcagggagtgggaggacccagccacaaa---gcaagagtgttggctgag------gcaatg---agccaagcaaac------------------------aatgtaaatata---atgatg------cagaaaagcaac---------ttc---aaaggtcctaaaagg---------attaaatgttttaactgtggcaaggaaggg---cacctagccaggaattgcagggcccctaggaaaaagggctgttggaaatgtgggaaagaaggacaccaaatgaaagactgt---------------acagagagacaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaacttccttcagaacaaaatagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggagct------------gaaagacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcaacgacccatggtctcaataaaagtagggggccagataaaagaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaagggctataggtacagtattagtgggacctacacctgtcaac---ataattggaagaaatatgttgactcagattggatgtacactaaattttccaattagtcccattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaaattaaacaa---tggccattgacagaagag---aaaataaaggcattaacagcaatttgtgaa------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccagtatttgccataaaaaagaaggatagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaacccaagacttttgggaa---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtaacagtactagatgtgggggatgcatat---ttttcagttcctttagatgaaaacttcaggaaatatactgcattcactatacctagtacaaacaatgaaactccaggaattagatatcaatataacgtgcttccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaaaatcctagagccctttagggcacaaaatccagaaatagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagggcaacatagagcaaagatagaagagttaagggaacatctattaaggtggggatttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctaccagaa---aaggat---agctggactgtcaatgatatacaaaagttagtgggaaaattaaactgggcaagtcagatttacccaggaattaaagtaaggcaactttgtaaactccttagaggggccaaagcactaacagacataataccactgactgaagaagcagaattagaattggcagaaaacagggaaattctaaaagaatcagtacatggagtatattatgatccctctaaagacttgatagctgaaatacagaaacaggggcatgaccaatggacctatcaaatttaccaagagccattcaaaaatctgaaaacaggaaagtatgcaaaaatg---aggagtgcccacactaatgatgtg------aaacagttaacagaggcagtgcaaaaaataaccatggaaagcatagtaatatggggaaag---actcctaaatttaaactacccatccaaaaagaaacatgggagacatggtgggcagactactggcaagccacctggattcctgagtgggagtttgttaatactcctcccctagtaaaattatggtaccagctggagaaagaacccatagcgggagtagaaactttctatgtagatggagcagctaatagggaaactaagataggaaaagcagggtatgttactgacagagggaggcagaaa---attgtctctctaactgaaacaacaaatcagaagactgaattacaagcaattcagttagctttacaagattcaggatcggaag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+>C.ZA.03.03ZASK076B1.AY901975
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+>C.ZA.03.03ZASK094B1.AY878070
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+>C.ZA.03.03ZASK097B1.AY878060
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+>C.ZA.03.03ZASK098B1.AY878061
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+>C.ZA.03.03ZASK104B1.DQ396395
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+>C.ZA.03.03ZASK107B1.DQ056410
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccaac-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------gcgaaagcgaaag------------------------------------------taagaccagagaa--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----gactggtgagtacgcc----------------------gaattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattacgcggcggaaaattagatgcatgggaaagaattaggcta---agg------cca---gggggaaagaaacaatataggctaaaacacctagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttggaaacatcagaaggctgtagacaaataatacaacagctacaaccagct---ctccagataggaacagaggagcttaaatcattatacaacacagta---gcaactctttattgtgtacatgaaaggatagaggtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaagtaag------------------------caaaaaacacagcaggcaaaagcg---------------------gctgacgga------------------------------aaa------------------------gtcagtcaaaattaccctata------------gtgcagaatcttcaagggcaaatagtacatcagtccttatcacctagaactttgaatgcatgggtaaaagtgatagaggagaag------gcttttaacccagagataatacccatgtttacagcactatcagaaggagccaccccacaagatttaaacaccatgttaaatacagtgggaggacatcaa---gcagccatgcagatg---ttaaaagat---accatcaatgaggaggctgcagaatgggatagattacat---ccagtccatgca---gggcctgttgcaccaggccaaatg---agggaacctaggggaagtgacatagcaggaactactagtacc---ctccaggaacaaatagcatggatgaca---------agtaaccca---cct---gtc---ccagtg---ggagacatctacaaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataagacaagggccaaaggaaccctttagagactatgtagaccggttctttaaaactctaagagccgaacaagctacacaagatgtaaaaaattggatgacagaaaccttgttggtccaaaatgcgaacccagattgtaagaccattttaagggcgttaggaccaggggcttcgttagaagaaatgatgacagcatgtcagggagtgggaggacctagccacaaa---gcaagagtgttggctgag------gcaatg---agccaaacaaac---------------------------agtaacata---atgatg------cagagaagcaat---------ttt---aaaggatttaaaaga------actgttaaatgcttcaactgtggcaaggaaggg---cacatagccagaaattgcagggctcctagaaaaaagggctgttggaaatgtggaaaagaaggacaccaaatgaaagactgt---------------accgagaggcaggctaattttttagggaaaatctggcc---ttcccagaa------ggg---ggg---gccagggaatttcctccagagcaggccagagccgacagc------------------------------------cccaccagtaccgacagccccaccagc------agagagcttcaggtt------------cgagga---agc---aac---ccccgc---------------------------------gag---------------gcaggagtc------------gaaggacaa---------------------------gga------------------------acccttaactgccctcaaatcactctttggcagcgacccatggtctcaataaaagtagggggccagataaaggaggctctattagacacaggagcagatgatacagtatta---gaagaa---ataaatttgtcaggaaagtggaaaccaagaatgataggaggaattggaggttttatcaaagtaagacagtgt---gatcaaatacttatagaaatttgtggaaaaaaggctataggtacagtattagtaggacctacaccggtcaac---ataattggcagaaatatgttgactcagcttggatgcacactaaattttccaattagccccattgaaactgtacctgtaaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagaa---gaaataaaagcattaacagcaatttgtgaa------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagc------actaagtggaggaaattagtagatttcagggaactcaataagagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagctggattaaaaaagaaa---aaa------tcagtgacagtgctagatgtgggggatgcatat---ttctcagttcctttagatgaaggcttcaggaaatatactgcatttaccatacctagtataaacaatgaaacaccaggaattagatatcaatataatgtgcttccacagggatggaaaggatccccagcaatatttcagagtagcatgacaaaaatcttagagccctttagagcacaaaatccagagatagtcatctatcaatatatggatgacttatatgtaggatctgacttagaaatagggcaacatagagaaaaaatagagaagttaagagaacatctattaagatggggattcaccacaccagataagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatagagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcaaatttatgcagggattaaagtaaggcaactttgtaaactccttaggggggccaaagcactaacagacatagtaccactaactgaagaagcagaattagaattagcagagaacagggagattctaaaagaaccagtacatggagtatattatgacccagcaaaagagttgatagctgaaatacagaaacaggggcaggatcagtggacatatcaaatttaccaagaaccattcaaaagtctgaaaacaggaaagtatgcaaaaaga---aggacagcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccatggaaagtatagtaatatggggaaag---actcctaaatttagactacccatccaaaaagaaacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagctggagaaagagcccatggcaggagtagaaactttctatgtagatggagcagctaacagggaaactaaaataggaaaagcagggtatgttactgacagaggaaggcagaaa---gtaattactctaactgagacaacaaatcagaagactgaattacaagcaattcagctagctctgcaagattcaggatcagaag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+>C.ZA.03.03ZASK111B1.DQ056404
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+>C.ZA.03.03ZASK113B1.DQ351237
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccatt-tctg-gttagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------tagaaccagagga--------gatctctcgacgca-gggctcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc----------------------aatttttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagagggggaaaattagatacatgggaaagaattaagtta---agg------cca---gggggaaagaaacattatatgctaaaacacctagtatgggcaagcagggagctggaaagatttgcacttaaccccggcctgttagaaaattcggaaggctgtagacaaatcttgaatcagctacaaccagct---cttcaaacgggaacagaggaacttagatcattatataacacagta---gcaactctctattgtgtacatgcaaaaatagatgtccgagacaccaaggaagccttagacaagatagaggaagaacaaaataaaagtaag------------------------caacaaaaacaacaagcagaagca------------------gctggcaaagga------------------------------aag------------------------gtcagtcaaaattatccaata------------gtgcagaatctccaagggcaaatggtacatcaggccatatcaccaagaactttaaatgcatgggtaaaagtaatagaggagaag------gccttcagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagacttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaggat---accatcaatgaggaggctgcagaatgggataggttacat---ccagtgcatgca---gggcctgtggcgccaggccaaatg---agagaaccaagaggtagtgacgtagcaggaactactagtaca---ctacaggaacaaatagcatggatgaca---------agcaaccca---cct---ata---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccccgtcagcattttggacataaaacaagggccaaaagaaccctttagagattatgcagaccgattctttaaaactttaagagctgaacaatctacacaagaggtaaagaattggatgaccgaaaccttgttggtccaaaatgcgaacccagattgtaagaccattttaagagcattaggatcaggggctacattagaggaaatgatgacagcatgtcagggagtgggaggacctggccacaaa---gcaagagttctggctgag------gcaatg---agccaagcaggc------------------------aaagtaaacata---atgatg------cagagaagcaat---------ttt---aagggccctaaaaga------gctattaaatgtttcaactgtggcaaggagggg---cacatagccaaaaattgcagggcccctaggaaaaaaggctgttggaaatgtggaaaggaaggacaccaaatgaaagactgt---------------actgaaaggcaggctaattttttagggaaagcttggcc---ttcccgcaa------ggg---gag---gccggggaatttccttcagagcagaccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcagga---------------------------------------------------gca------------gcaaga---accacccttaacttccctcaaatcactctttggcaacgaccccttgttacaataaaagtagagggccagataatggaggctctcttagatacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gagcaaatacatatagaaatttgtgaaaaaaaggctataggtacagtattagtaggacctacacctgccaac---ataattggaagaaatattttgactcagcttggatgcacaataaattttccaattagttccattgacactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagcaatctgtgaa------gacatggagaaggaaggaaaaatttcaaaa---attgggcct---gaaaatccatataacactccagtatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttgggaa---gtccaa------tta---ggaata---------------------------ccacacccagcagggctaaaaaagaaa---aaa------tcagtgacagtgctggatgtgggggatgcatat---ttttcagttcctttagatgaaagcttcaggaaatatactgcattcaccatacctggtataaacaatgaaacaccagggattagatatcaatataatgtgcttccacagggatggaaaggatcaccatcaatattccagagtagcatgacaaaaatattagagccctttaggacacaaaatccagacatagttatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaggagttaagggaacatttattgaaatggggatttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgagctccatcctgacaaatggacagtgcagcctatactgttgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggccagccagatttacccagggattaaggtaaggcaactgtgcaaactccttaggggagccaaagcactaacagacatagtaccactgactgaagaagcagaattagaattggcagaaaacagggaaattctaaaagaaccagtacatggagcatattatgacccctcaaaagacttaatagctgaaatacagaaacaagggcgtgaccaatggacatatcaaatttaccaagaaccatttaaaaatctgaaaacagggaagtatgcaaaattg---aggactgcccacaccaatgatgta------aaacagttaacagaagcagtgcaaaaaatagctctagaaagcatagtaatatggggaaag---actcctaaatttagattacccatccaaaaggaaacatgggaaacgtggtggacagactattggcaagccacctggatccctgagtgggagtttgtcaatacccctcccctagtaaaattatggtaccaactggaaaaagagcccatagcaggagcagaaactttctatgtagatggagcagctaatagggagactaaactagggaaagcagggtatgttactgacaaaggaagacagaaa---gttgtttcgctaactgaaacaacaaatcagaaggctgagttacaagcaattcagctagctttacaggattcaggattagaag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+>C.ZA.03.03ZASK211B1.DQ093601
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccttt-tgtg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaaacgaaag------------------------------------------tagaaccagagaa--------gatctctcgacgca-agactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----gactggtgagtacgcc----------------------aatttttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagaggcgaaaaattagataaatgggaaaaaattaggtta---agg------cca---gggggaaagaaacaatatatgataaaacacatagtatgggcaagcagggagctggaacgatttgcacttaaccctggccttttagaaacatcagaaggccgtagacaaataatgaaacagctacaaccagct---cttcagacaggaacagaggaacttaggtcattatacaacacagta---gcaactctctattgtgtacatgaaaatatagatgtaagagacaccaaggaagccttagacaaaatagaggaagaacaaaacaaaagtcag------------------------caaaaaacacagcaggcaaaagcg---------------------gctgaagga------------------------------aag------------------------gtcagtcaaaattaccctata------------gtgcagaatctccaagggcaaatggtacatcaggccatatcacctagaaccttgaatgcatgggtaaaagtaatagaggaaaag------gcctttagcccagaggtaatacccatgtttacagcactatcagaaggagccaccccatcagatttaaacaccatgttaaatacggtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaggaggctgcagaatgggatagactacat---ccagtacatgca---gggcctgttgcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactaccagtacc---cttcaggaacagatagcatggattaca---------gctaaccca---cct---att---ccagtg---ggagaaatctataaaagatggataattctggggctaaataaaatagtgagaatgtatagccctgtcagcattttggacataaaacaagggccaaaagaaccctttagagactatgtagatcggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaatcggatgacagacaccttgttggtccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccaggggcttcattagaagaaatgatgacagcatgccagggagtgggaggacctagccacaaa---gcaagagtgttggctgag------gcaatg---agccaagcaaac------------------------agtggaaacata---atgatg------cagagaaacaac---------ttt---aaaagttctaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccagaaactgtagggcccctaggaaaaagggctgttggaaatgtggaaaggaaggacatcaaatgaaagactgt---------------actgagaggcaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagaacagaccagagccaacagc------------------cccaccagcagggagcttcagactagagccaacagccccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggagct------------gaaagacag---------------------------gga------------------------agccttaacttccctcaaatcactctttggcaacgaccccttgtctcaataaaagtagggggccagataaaggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacttatagaaatctgtggaaaaaaggctataggtacagtactagtagggcctacacctgtcaac---ataattggaagaaatatgttgactcagcttggatgcacgttaaattttccaattagccccattgaaactgtaccagtacaactaaagccaggaatggatggcccaaaggttaaacaa---tggccattgactgaagaa---aaaataaaagcattaaaagcaatttgtgaa------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacaccccagtatttgccataaaaaagaaggatagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaag---aag------tcagtgacagtactggatgtgggagatgcatat---ttttcagtacctttatatgaagacttcaggaaatatactgccttcaccatacctagtacaaacaatgaaacaccagggattagatatcagtataatgtgctcccacaaggatggaaaggatcaccagcaatattccagtgtagcatgacaaaaatcttagagccctttagagcaaaaaatccaggaatagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagggcaacatagggcaaaaatagaggagttaagagaacatctattaaaatggggatttaccacaccagacaagaaacatcaaaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtgcagcctatacagctgccagaa---aaagat---aactggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacccaggggttagagtaaagcacctttgtaaactcctaagaggggtcaaagcactaacagacatagtaccactaactgaagaagcagaattagaattggcagagaacagggaaattctaaaagaaccagtacatggagtatattatgatccatcaaaagacttgatagctgaaatacagaaacaggggcatgaccaatggacatatcaaatttaccaagaaccattcaagaatctgaaaacagggaagtatgcaaaaagg---aggactgcccacacaaatgatgtg------aaacagttaacagaggcagtgcgaaaaatagcaatggaaagcatagtaatatggggaaag---actcctaaatttagactacccatctcaaaagaaatatgggagacatggtggacagactattggcaggccacctggattcctgagtgggagtttgttaatacccctcccctagtaaagttatggtatcagttggaaaaagaacccatagcagaagcagaaactttctatgtagatggagcagctaatagggaaactaaaataggaaaagcagggtatgttactgacagaggaaggcaaaaa---attgtttctctaagtgaaacaacaaaccagaagactgaattacaagcaattcaattagctttacaagattcaggatcagaag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+>C.ZA.03.03ZASK213B1.DQ093607
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccctt-tgtg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ctgaaagcgaaag------------------------------------------tgagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------gaga-gg--cggc-----ggcgggtgagtacgcc----------------------aaattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggaggaaaattagatacatgggaaaaaatcaggtta---agg------cca---gggggaaagaaacactatatgctaaaacacatagtatgggcaagcagggagctggaaagatttgcacttaaccctggtcttttggaaacagcagaaggctgtaaacaaataataagacagctacaaccagct---ctccagacaggaacagaggagcttcgatcattatttaacacagta---gcaactctctattgtgtacatgcgaagatagaggtacgagacaccaaggaagccttagacaagatagaggaagaacaacgcaaatgtcag------------------------caaaaaacacagcaggcagaagca------------------gctgacaaagga------------------------------aag------------------------gttagtcaaaattatccaata------------gtacagaatgcccaagggcaaatggtacaccagcccatatcacctaggactttaaatgcatgggtaaaagtgatagaggagaaa------gcttttagtccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagacttaaacaccatgttaaatacagtgggaggacatcaa---gcagccatgcagatg---ttaaaagat---accatcaatgagggggctgcagaatgggataggatacat---ccagtgcatgca---gggcctgttgcaccaggccaaatg---agagagccaaggggaagtgacatagcaggaactactagtacc---ctggcggagcaaatagcatggatgaca---------ggtaaccca---cct---atc---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaagggccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagggctgaacaagctacacaagatgtaaaaaattggatgacagagaccttgttaatccaaaatgcgaacccagattgtaagacaattttaagagcattaggagcaggggctacactagaagaaatgatgacagcatgtcagggagtgggaggacctggccacaaa---gcaagagtattggctgag------gcaatg---agccaagcaaac------------------------aatgcaagcata---ctaatg------cagagaggcaat---------ttt---aaaggccctaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccagaaattgcagggcccctaggaaaaaaggctgttggaaatgtggaaaggaaggacaccaactgaaagattgt---------------actgaaaggcaggccaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagaacaggccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---gac---ccctgc------------------------------tccgaa---------------gcaggagat------------gaaagacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggccagctaaaagaggctctcttagatacgggagcagatgatacagtatta---gaagaa---atgagtctaccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacctatagaaatttgtggaaaaaaggctatagggacagtattaatagggcctacacctgtcaac---ataattggaaggaatctgttgactcagcttggctgtacactaaattttccaattagtcccattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaggtcaaacaa---tggccattgacagaagag---aaaataaaagcattaacagaaatttgtgaa------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataatacaccagtatttgccataaaaaagaaagacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaag---aaa------tcagtgacagtactagacgtgggggatgcatat---ttttcagttcccttagatgaaagcttcaggaaatatactgcattcaccatacctagtacaaacaatgaaacaccagggattagatatcaatataatgtgctgccacagggatggaaaggatcaccagcaatattccagtgtagcatgacaaaaatcttagagccctttagagcaaaaaatccagaaattgtcatctatcaatatatggatgacttgtacgttggatctgacttagaaatagggcaacatagggcaaaaatagaggagttaagagcacatctattaaagtggggactcaccacaccagacaagaaacatcaaaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agttggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttatccaggaattaaaataaaacaactttgtaaactccttaggggggccaaagcactaacagacatagtaccactaactgaagaagcagaattagaattggcagagaacagggaaattctgaaagaaccagtacatggagtgtattatgacccatcaaaagacttgatagctgaaatacagaaacagggtaatgaccaatggacatatcaaatttaccaagaaccattcaaaaatctgaaaacaggaaagtatgcaaaaatg---aggactgcccacactaatgatgta------agacagttaacagaggcagtgcaaaaaatagccctggaaagcatagtaatatggggaaag---agtcctaaatttagactacccatccaaaaggaaacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatactcctcccctagtgaagttatggtaccagctggagaaagaacccatagcaggagcagaaactttctatgtagatggagcagctcatagagagactaaaacaggaaaagcagggtatattactgacaagggaaggcaaaaa---attgtttctctaaatgaaacaacaaatcagaaggctgagttacaagcaattcagctagctttgcaggattcaggattagaag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+>C.ZA.03.03ZASK215M6W.DQ275661
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+>C.ZA.03.03ZASK223B1.DQ093597
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccaac-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ccgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----gactggtgagtacgcc----------------------gaattttatttgact----------agcgga-gg---------ctagg-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggcgaaaaattagatgcatgggaaagaattaggtta---agg------cca---gggggaaagaaacattatatgctaaaacacctagtatgggcaagcagggagctggatagatttgcacttaaccctggccttttagagacatcagaaggctgtaaacaaataataagacagctacaaccagct---cttaagacaggaacagaggaacttaaatcattattcaacacagta---gcaactctttactgtgtacatgaaaggatagaagtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaattcag------------------------caaaaagcacagcaggcaaaagcg---------------------gctgacggg------------------------------aaa------------------------gtcagtcaaaattaccctata------------gtacagaatctccaagggcaaatggtacaccagcccatatcacctagaactttgaatgcatgggtaaaagtaatagaggagaag------gcttttagcccggaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcagatg---ttaaaagat---accatcaatgaggaggctgcagagtgggatagattacat---ccagtccatgca---gggcctattgcaccaggccaaatg---agggaacctaggggaagtgacatagcaggaactactagcacc---cttcaggagcaaatagcatggatgaca---------ggaaaccca---cct---gtt---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataagacaagggccaaaggaaccctttagagactatgtagaccggttctttaaagtcttaagagctgaacaagctacacaagatgtgaaaaattggatgacagaaaccttgttggtccaaaatgcaaacccagattgtaagaccattttaagggcattaggaccagcagctacattagaagaaatgatgacagcatgtcagggagtgggaggacctagccacaaa---gcaagagtgttggctgag------gcaatg---agccaagcaaac---------------------------aataccgta---ctgatg------cagaggagcaat---------gtt---aaaggacctagaaga------actgttaaatgcttcaactgtggcaaggaaggg---cacatagccagaaattgcagggctcctaggaaaaagggctgttggaaatgtggaaaagaaggacaccaaatgaaagattgt---------------actgagaggcaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagagcaggccagagccgacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccctgc------------------------------tccgaa---------------gcaggaatc------------gaaagacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgaccccttgtcacaataaaagtagggggccagataaaggaagctctattagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacctatagaaatttgtggaaaaaaggctataggtacagtattagtagggcctacacctgtcaac---ataattgggagaaatatgttgactcagcttggatgcacactaaattttccaattagccctattgaaactgtaccagtaaaattaaagccaggaatggacggcccaaaggttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagcaatttgtgaa------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagt------actaagtggaggaaattagtagatttcagggaactcaataaaagaacacaagacttttgggaa---gttcaa------tta---ggaatt---------------------------ccacacccagcaggattaaaaaagaaa---aaa------tcagtgacagtactagatgtgggggatgcatat---ttttcagttcctttagatgaaagcttcaggaaatatactgcatttaccatacctagtataaacaatgaagcaccaggaattagatatcaatataatgtgcttccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaaaattttagagccctttagagcaaaaaatccagaaatagtcatctatcaatatatggatgacttatatgtaggatctgacttagaaatagagcaacatagagcaaaaatagaggagttaagagaacatctattgaagtggggattcaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgagctccatcctgacaaatggacagtacagcctataaagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacccagggattaaagtgaggcaactttgtaaactccttaggggggccaaagcattaacagacatagtaccactaactgaagaagcagaattagaattggaagagaatagggaaattctaaaagaaccagtgcatggagtatattatgacccagcaaaagatttgatagcggaaatacagaaacaggggcaggatcaatggacatatcaaatctaccaagaaccatttaaaaatctgaaaacagggaagtatgcaaaaagg---aggacggcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagcccaggaaagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaagagacatgggaaacatggtggacagattattggcaagctacctggattcctgagtgggagtttgttaatacccctcccctggtaaaattatggtaccagctggagaaagagcccatagcaggagtagaaactttctatgtagatggagcagctaatagggaaactaaattaggaaaagcagggtatgttactgacagaggaaggcagaaa---gttattactctaactgaaacaacaaatcagaagactgaattacaagcaatccagctagctttgcaagattcaggatcagaag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+>C.ZA.03.03ZASK224MB1.DQ275664
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------gctagagatc-------cctcagacca-t-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------cagaaagcgaaag------------------------------------------caagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc----------------------aatttttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggcgaaaagttagataaatgggaaaaaatcaggtta---agg------cca---ggaggaaagaaacattatatgttaaaacacttagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacatcagaaggctgtaaacaaataataaaacagctacaaccagct---cttcagacaggaacagaggaacttagatcattatacaacacagta---gcaactctctattgtgtgcatagagggatagaggtacgagacaccaaggaagccttagacaggataggagaagaacgaaacaaaagtcag------------------------caaaaggcacagcaagcagaagcg------------------gctgataaagga------------------------------aaa------------------------gtcagtcaaaattatccaata------------gtgcagaatctccaagggcaaatggtacaccagcccatatcacctagaactttaaatgcatgggtaaaagtaatagaggaaaag------gctttcagcccggaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---acaatcaatgaggaggctgcagaatgggatagattacat---ccagtacatgca---gggcctattgcaccaggccaaatg---agagacccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------aataaccca---cct---gtt---ccagtg---ggagacatctataaaagatggataattctggggctaaataaaatagtaagaatgtatagccctgtcagcattttggacataagacaaggaccaaaggaaccctttagggactatgtagaccggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagagaccttgttagtccaaaatgcgaacccagattgtaagaccattttaaaagcattaggaccaggggcttcattagaagaaatgatgacagcatgccagggagtgggaggacctggccacaaa---gcaagagtgttggctgag------gcaatg---agccaaacaaac---------------------------agtagcata---ctgatg------cagagaagcaat---------ttt---aaaggcgctaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccaaaaattgcagggcccctaggaaaaaaggctgttgggaatgtggacaagaaggacaccaaatgaaagaatgt---------------cccggaaggcaggctaattttttagggaaaatctggcc---ttccaacaa------ggg---gag---gccagggaatttccttcagagcagaccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---aac---aac---ccctgc------------------------------tccgaa---------------gcaggagcc------------gaaagacag---------------------------gga------------------------acctttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtaggggggcagataaaggaggctctcttagatacaggagcagatgatacagtatta---gaagaa---ataaatctaccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaaaggctataggtacagtattagtaggacctacacctgtcaac---ataattggaagaaatatgttgactcagcttggatgtacgctaaattttccaattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggccctaaggttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagcaatttgtgaa------gaaatggagaaggagggaaaaattacaaaa---attgggcct---gaaaatccatataacacgccagtatttgccataaaaaagaaagatagt------actaagtggagaaaattagtagatttcagagaactcaataaaagaactcaagacttttgggaa---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaagaagaaa---aaa------tcagtgacagtactggatgtgggggatgcatat---ttttcagttcctttagatgaaggcttcagaaaatatactgcattcaccatacctagtataaacaatgaaacaccagggattagatatcaatataatgtgctaccacagggatggaaaggatcaccagcaatattccagagtagcatgacaagaatcttagagccctttagagcacaaaatccagaagtagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagggcaacatagagcaaaaatagagcagttaagagaacatctattaaagtggggacttaccgcaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacggtgcagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacaaaagttagtaggaaaattaaactgggcaagtcagatttacccagggattaaagtaagacaactctgtaaactccttaggggggccaaagcactaacagacatagtaccactaactggagaagcagagttggaattagcagaaaacagggaaattctaaaagaaccagtacatggagtatattatgacccatcaaaagaattgatagctgaaatacagaaacagggggattaccaatggacatatcaaatttaccaagaaccattcaaaaatctgaaaacagggaagtatgcaaaaatg---agaactgcccacaccaatgatgta------aaacagctaacagaggcagtgcaaaaaatagctctagaaagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaggaaacatgggagacatggtggacagactattggcaagccacctggatccctgagtgggagtttgtcaacacccctcccctagtaaaattatggtaccaactggaaaaagaacccatagcaggggcagaaactttctatgtagatggagcagctaatagggacactaagttaggaaaagcagggtatgttactgacaaaggaaggcagaaa---attgtttctctaactggaacaacaaatcagaaggctgagttacaagcaatccagctagccttacaggattcaggattagaag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+>C.ZA.03.03ZASK226B1.DQ164108
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagatcctt-tttg-g-ctgtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagtgaaag---------------------------------------taagaccagagaagaa--------gaactctcgacgca-gggctcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--gggc-----gactggtgagtacgcc-----------------------aattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagagggggaaatttagataaatgggaaaaaattaggtta---cgg------cca---gggggaaagaaacaatataggctaaaacacttagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacatcagaaggctgtagacaaataataaaacagctacaaccagct---attcagacaggaacagaggaacttaaatcattgtacaacacagta---gcaactctctattgtgtacatgaaggcatagaggtacgagacaccaaggaagccttagacaaaatagaggaagaacagaacaaaagtcag------------------------caaaaaacacagcaggcaaaagcg------------------gctgacaaaaaa---------------------------------------------------------gtcagtcaaaactatcctata------------gtgcagaatatccaaggacaaatggtacaccaggccatatcacctagaactttaaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacgggatttaaacaccatgttaaacacagtggggggacatcaa---gcagccatgcagatg---ttaaaagat---accatcaatgaggaggctgcagaatgggatagattacat---ccagtacaggca---gggcctgttgcgccaggccaaatg---agggatcctaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------agtaaccca---cct---gtc---ccagtg---ggagaaatatataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaagggccaaaggaaccctttagagactatgtagatcggttctttaaggttttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaacccagattgtaaaaccatcctaagagcattaggaccaggggctacattagaagaaatgatgacagcatgtcagggagtgggaggacctagccacaaa---gcaagagtgctggctgag------gcaatg---agccacgcaaac---------------------------aataccata---atgatg------cagagaggcaat---------ttt---aaaggagctaaaaga------attgttaaatgcttcaactgtggcaaggagggg---cacatagccaaaaattgcagggcccccggaaaaaagggatgttggaaatgtggaaaagaaggacaccagatgaaagactgc---------------attgagaggcaggctaattttttagggaaaatttggcc---ttcctacaa------ggg---gag---gccagggaatttccttcagaacagaccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaagtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggagtc------------gaaaggcag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtaggaggtcaggtaaaagaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccagggaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaaaggctataggtacagtattagtaggacctacacctgtcaac---ataattggaagaaacatgttgactcagcttgggtgcacattaaattttccaattagccccattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagcaatttgtgaa------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccgtataacactccaatatttgctataaaaaagaaggacagt------actaagtggaggaaattagtggattttagggaacttaataaaagaactcaagatttttgggag---gttcaa------tta---ggaata---------------------------ccgcacccagcaggattaaaaaagaaa---aaa------tcagtgacagtgctggatgtgggggatgcatat---ttttcagttcctttagataaaggcttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccagggattagatatcaatataatgtgcttccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaaaatcttagagccctttaggacacaaaatccagaaatagtcatctatcaatatatggacgacttatatgtaggatctgatttagaaatagggcaacatagagcaaaaatagaggagttaagagaacatctattgaggtggggattcaccacaccagataagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctataaagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacccagggattaaggtaaagcaactctgtaaactccttaggggggtcaaagcattaacagacatagtaccactaactgaagaagcagaattagaattagcagagaacagggaaattctaaaagaaccagtacatggggtatattatgacccatcaaaagatttaatagctgaagtacagaaacaggggcatgaccaatggacatatcaaatataccaagaaccattcaaaaatctgaaaacagggaagtatgcaaaaagg---aggacgacccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccatggaaagcatagtaatatggggaaag---acccctaaatttagactacccatccaaaaagaaacatgggagacatggtggacagattattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttggtaaaattatggtaccagctggagaaagaacccctggagggagtagaaactttctatgtagatggagcagctaatagggaaactaaaataggaaaagcagggtatgttactgatagaggaaggcagaaa---gttgttaccataactgaaacaacaaaccagaagtctgaattacaagcaattcagctagctttgcaagattcaggatcagaag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+>C.ZA.03.03ZASK232B1.DQ093589
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccctt-cgtg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------tcgaaagcgaaag------------------------------------------taagaccagagca--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc------------gaggggag--cggc-----ggctggtgagtacgcc---------------------aaacttttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaaaagggggaaaattagatgaatgggaaaaaattaggttg---agg------cca---gggggaaagaaacactatatgataaaacacctagtatgggcaagcagggagctggaaaaatttgcacttaaccctggccttttagagaactcagaaggctgtaaacaaacaataaaacagctacacccagct---cttcagacaggaacagaggaacttaaatcattatataacacagta---gcaactctctattgtgcacatgaaaagataaaggtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaatgtcag------------------------ctaaaagcacagcaagcagaagcg------------------gctgacaaagga------------------------------aag------------------------gtcagtctaaattatcctata------------gtgcagaatctccaggggcaaatggtacatcagcccctttcaccgagaactttaaatgcatgggtaaaggtaatagaggagaag------gctttcagcccagaggtaatacccatgtttacagcattatcagaaggagccacccctcaagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaagaggctgcagactgggatagggtgcat---ccagtacaggca---gggcctgttgcaccaggccaaata---agagaacccaggggaagtgacatagcaggaaccactagtacc---cttcaggaacaaataacatggatgaca---------aataaccca---cct---att---ccagta---ggagaaatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaaggaccaaaagaaccctttagagactatgtagaccggttcttcaaaaccttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaacccagattgtaagaccattttaagggcattaggatcaggggctacattggaagaaatgatgacagcatgtcaaggagtgggaggacctagccacaaa---gcaagagttttggctgag------gcaatg---agccaggcaaac------------------------catacaaacata---atgatg------cagagaagcaat---------ttt---aaaggccctaaaaga------attattaaatgcttcaactgtggcaaagaaggg---cacatagccaaaaattgcagggcccccaggaagaagggctgttggaaatgtggaaaggaaggacaccgaatgaaagactgt---------------actgagaggcaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttcctccagagccgaccagagccaacagc------------------------------------------------------cccaccagc------agagggtttcagttt------------cgagga---aac---acc---ccctgc------------------------------tccgag---------------gcaggagcc------------gaaaaacag---------------------------gga------------------------acctttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggccaaacaagggaggctctcctagatacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gaccaaatactcatagaaatttgtggaaaaaaggctataggtacagtattagtaggacctacacctgtcaac---ataattggaagaaatatgttgacacagcttggatgcacactaaattttccaattagtcctattgaaactgtaccagtaaagttaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattgacagcaatttgtgaa------gaaatggaaaaagaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaagacagt------actaagtggagaaaattagtagacttcagggaacttaataaaagaactcaagacttttgggaa---gttcaa------tta---gggata---------------------------ccacgcccagcagggttaaaaaagaaa---aaa------tcagtgacagtgctggatgtgggggatgcatat---ttttcaattcctttagatgaaagcttcaggaaatatactgcattcaccatacctcgtacaaacaatgcgacaccaggaattagatatcaatataatgtgcttccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaaaatcttagagcccttcaggacaagaaacccagaactagttatctatcaatacatggatgacttgtatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaggagttaagagaacatttattgaaatggggacttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgataaatggacagtacagcctatacagctgccggac---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacccagggatcagagtaaggcacctgtgtaaactccttaggggagccaaagcactaacagacatagtaccactgactgaagaagcagaattagaattggcagagaacagggaaattctaaaagaaccagtacatggggtatattatgacccatcaaaagacttaatagctgaaatacagaagcaggggcatgaccaatggacatatcaaatttaccaagaaccattcaaaaatttgaaaacaggaaagtatgcaaaaatg---aggactgcccacaataatgatgta------aaacaattagcagaagcagtgcaaaaaataaccatggaaagcatagtaatatggggaaag---actcctaaatttagactgcccatccaaaaagacacatgggagacatggtgggcagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtatcaactggagaaagaacccataataggagcagaaactttctatgtagatggagcagctaatagagaaactaaattaggaaaagcagggtatgttactgacaaaggaagacaaaag---gtcgtttctctaactgaaacaacaaatcagaaggctgaattaatagcaattcggctagctttacaggattcaggattagaag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+>C.ZA.03.503_14197_T1.KT183301
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+>C.ZA.03.SK023B2.AY772690
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+>C.ZA.03.SK029B2.AY772691
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+>C.ZA.03.SK040B1.AY703908
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+>C.ZA.03.SK041B1.AY772693
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+>C.ZA.03.SK116B1.AY772696
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+>C.ZA.04.04ZAPS160B1.DQ164107
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+>C.ZA.04.04ZAPS161B1.DQ164115
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccttt-tgtg-t-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------gcgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--gggc-----gactggtgagtacgcc----------------------aatttttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggcgaaaaattagataaatgggaaagaattaggtta---agg------cca---gggggaaagaaacattatatgttaaaacacatagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacatcagaaggctgtaaacaaatactgatacagctacaaccagct---cttaagacaggaacagaggaacttaaatcattatacaacacagta---gcaactctctattgtgtacataaagggatagatgtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaagtcag------------------------caaaaaacacagcaggcaaaagcg---------------------gctgacggg------------------------------aaa------------------------gtcagtcaaaattatcctata------------gtgcagaatctacaagggcaaatggtacatcaagccctatcacctagaaccttgaatgcatgggttaaagtaatagaggaaaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacggtggggggacatcaa---gcagccatgcaaatg---ttaaaggat---accatcaatgaagaggctgcagaatgggatagagtacat---ccagtccatgcg---gggccagttgcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacagatagcatggatgaca---------agtaaccca---cct---gct---ccagtg---ggagagatctataaaagatggataattctggggttaaataaaatagtgagaatgtacagccctgtcagcattttggacataagacaagggccaaaggaaccctttagagattatgtagatcggttcttcaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagaaaccttgttggtccaaaatgcaaacccagattgtaagaccattttaagagcattaggaccaggggccacattagaagaaatgatgacagcatgtcagggagtgggaggacctggccacaag---gctagggtgttggctgag------gcaatg---agccaagcaaac------------------------agtaaaaacata---atgatg------cagagaagcaat---------ttt---agaggctctaaaaga------attgtcaaatgtttcaactgtggcaaggaaggg---cacatagcaagaaactgcagagctcctaggaaaaagggctgttggaaatgtggaagggaaggacaccaaatgaaagactgt---------------actgagaggcaggctaattttttagggaaagtctggcc---ttcccagaa------ggg---gag---gccgggaaatttccttcagaacagaccagagccaacagc------------------cccaccagcagagagcttcaggtgcgagccaacagccccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccccgc------------------------------cccgaa---------------gcaggagcc------------gaaagacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggtcaggtaagagaggctctcttagatacaggagcagatgatacagtatta---gaagac---ataaatttgtcagggaaatggaaaccaagaatgataggaggaattggaggttttatcaaagtaagacagtat---gatgaaatagctatagaaatttttggaaaaaaggctataggtacagtattagtagggcctacacctgtcaac---ataattgggagaaatatgttgactcagcttggatgcacactaaattttccaattagttccattgaaactgtaccagtgaagctaaaaccagggatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacagaaatttgtaat------gaaatggagaaagaaggaaaaatttcaaaa---attgggcct---gaaaatccatataacaccccaatatttgccataaaaaagaaggacagt------actaagtggagaaagttagtagatttcagggaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtgacagtattggacgtgggggatgcatat---ttttcagttcctttagataaggaattcaggaaatatactgcattcaccatacctagcataaacaatgagacaccagggattagatatcaatacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaagaatcttagagccctttagagcaaaaaatccagaaatagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagaacaacatagagcaaaggtagaggagctaagagaacatctattaaagtggggacttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctaccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacccagggattaaagtaaggcaactttgtaaactccttagagggaccaaagcgctaacagacatagtagcactaactgaagaagcagaattagaattagcagagaacagggaaattctaaaagaaccagtacatggagtatattatgacccatcaaaagacttgatagctgaaatacagaaacagggacatggtcaatggacatatcaaatttaccaagaaccattcaaaaatctgaaaacagggaagtatgcaaaaatg---aggactgcccacactaatgatgta------aaacagctagtagaggcagtgcaaaaaatagccatagaaagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaagaaacatgggacatatggtggacagattattggcaagccacctggattcctgagtgggagtttgttaatactcctcccctagtaaaattatggtaccagctggagaaagaccccatagtaggagcagaaactttctatgtagatggagcagctaatagggaaaccaaaatgggaaaagcagggtatgttactgacaaaggaaggcaaaag---attgttactctaactgaaacaaccaatcagaaaactgaattacaagcaattcagctagctttgcaagattcaggatcagaag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+>C.ZA.04.04ZAPS165MB1.DQ351221
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagacctat-attg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--gggc-----gactggtgagtacgcc----------------------aatttttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggggaaaaattagatatgtgggaaaaaattaggtta---agg------cca---gggggaaagaaatgttatatgttaaaacacatagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaaactcagagggctgtaaacaaataatgagacagctacagccagct---cttcagacaggaacacaggaacttagatcattatacaacacagta---gcaactctctattgtgtacatgaaaagatagatgtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaagtcag------------------------cagaaaacacagcaggcaagagcg---------------------gctgacgga------------------------------aag------------------------atcagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtacatcaacccttatcacctagaaccttgaatgcatgggtaaaagtagtagaggaaaag------ggttttaacccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaataccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---actatcaatgaagaggctgcagaatgggatagattacat---ccagtacatgcg---gggcctattcaaccaggtcaaatg---agagaaccaaggggaagtgacatagcaggaactactagtaac---cttcaggaacaaataaattggatgaca---------ggtaacccg---cct---att---ccagtg---ggagaaatctataaaagatggatagttctggggttaaataaaatagtgagaatgtatagccctgtcagcattttggacataaaacaagggccaaaggaaccctttagagactatgtagatcggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaacccagattgtaagactattttaagagcattaggaccagcagctacattagaagaaatgatgacagcatgtcagggagtgggagggcctggccacaaa---gcaagagtgctggctgag------gcaatg---agccaagcaaac------------------------aatataagtgta---ttgatg------cagagaggtaat---------ttt---aaaggctctaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccagaaattgcagagcccctaggaaaaaaggctgttggaagtgtgggaaggaaggacaccaaatgaaagactgt------------acttatgagaggcaggctaattttttagggaagatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagggcagaccagagccaacagc---------------------------------cccaccagcagagccaacggccccaccagt------agagagcttcaagtt------------cgaggg---gac---aaa---ccccgc------------------------------tctgaa---------------gcaggagca------------gaaagacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggtcaggtaaaggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacgtatagaaatttgtgggaaagaggctataggtacagtattagtagggcctacacctgtcaac---ataattggaagaaatatgttgactcagcttggatgtacactaaattttccaattagtcccatcgaaactgtaccagtaaaactaaagccaggaatggatggcccaaaggttaaacaa---tggccattaacagaagag---aaaataaaagcattaacagcaatttgtgag------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactcccatatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaacttaataaaagaactcaagatttttgggag---gttcaa------tta---ggaata---------------------------ccacatccagcagggttaaaaaagaaa---aaa------tcagtgacagtactggatgtgggagatgcatat---ttttcagttcctttagatgaaggcttcagaaaatatactgcattcaccatacctagtacaaacaatgaaacaccagggattagatatcaatataatgtgctcccacaaggatggaaggggtcaccagcaatattccagagtagcatgacaaaaatcttagagccttttagagcaaaaaatccagaaatagtcatctatcaatatatggatgacctgtatataggatctgacctagaaatagggcaacatagagcaaagatagaggagttaagagaacatctattaaaatggggatttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgataaatggacagtacagcctatacagttgccagaa---aaagat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacccagggattaaagtaaagcaactttgtaaactccttaggggagccaaaacactaacagacatagtaccgctaactgaagaagcagaattagaattggcagagaacagggaaattctaaaagaaccagtacatggagtatattatgacccatcaaaagacttgatagctgaaatacagaaacagggggatgaccaatggacatatcaaatttaccaggaaccattcaaaaatctgaaaacagggaagtatgcaaaaaag---aggacagcacacactaatgatgta------aaacagttaacagaggcagtacaaaaaatagccttagaaagcatagtaatatggggaaag---attcctaaatttagattacccatccaaaaagaaacatgggagatatggtggacagactattggcaagccacctggattcccgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagctggagaaagaacccatagcaggagcagaaactttctatgtagatggagcagctagtagggaaactaaaatgggaaaagcagggtatgttactgacagaggaaggcagaaa---attgtttccctaactgagacaacaaatcagaagactgaattacaagcaattcagctagctttgcaagattcaggatcagaag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+>C.ZA.04.04ZAPS169MB1.DQ396393
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+>C.ZA.04.04ZAPS172MB1.DQ275659
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+>C.ZA.04.04ZAPS177MB1.DQ396394
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+>C.ZA.04.04ZAPS188B1.DQ164122
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccttt-tgag-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ctgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc-----------------------aattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaaaaggcggaaaattagatgcatgggaaaaaattaggtta---agg------cca---gggggaaagaaacactataggctaaaacacctagtatgggcaagcagggagctggaaagatttgcacttaaccctggtcttttagaaacatcagaaggctgtaaacaaataataagacagctacatccagct---ctccagacgggaacagaggaacttaagtcattatataacacagta---gtagttctctattgtgtacacgaaaagatagaggtccgagacaccaaagaggccttagacaagatagaggaagaacaaaacaaaagtcag------------------------caaaaaacacagcaggcaaaagcg---------------------gctggcggg------------------------------aac------------------------gtcagtcaaaattatcctata------------gtacagaatctccaagggcaaatggtacaccaggccttatcacctagaactttgaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaggtaatacccatgttcacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcagatg---ttaaaagat---accatcaatgaggaggctgcagaatgggacagattacat---ccagtccatgca---gggcctattgcaccaggccaaatg---agggaacctaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------aataaccca---cct---gtc---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaggggccaaaggaaccttttagagactatgtagatcggttctttaaagttttgagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcaaacccagattgtaagaccattttaagggcattaggaccagcggcctcattagaagaaatgatgacagcatgtcagggagtgggaggacctggccacaaa---gcaagagtgttggctgag------gcaatg---agccaagcaaac---------------------------agtaacata---atgatg------cagagaagtaat---------ttt---aaaagatctaaaaga------attgttaaatgcttcaactgtggcaaggacggg---cacatagccagaaattgcagggcccctaggaaaaaaggctgctggaaatgtggaaaagaaggacaccaaatgaaagactgt---------------actgagaggcaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagagcaggccagagcctacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---cac---ccccgc------------------------------tccgaa---------------gcaggagtc------------gaaagacaa---------------------------gga------------------------acccttaatttccctcaaatcactctttggcagcgacccctagtctcaataaaagtagggggccagataaaggaggctctattagatacaggagcagatgatacagtgtta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaaaggctacaggtacagtattagtaggacctacacctgtcaac---ataattggaagaaatatgttgactcagcttggatgcacgctaaattttccaattagccccattgaaactgtaccagtaaaattaaaaccaggaatggatgggccaaaggttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagcaatttgtgaa------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagt------actaagtggaggaaattagtagatttcagggaactcaataaaagaactcaagatttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcaggattaaaaaagaaa---aaa------tcagtgacagtactggatgtgggggatgcatat---ttttcagttcctttagatgaagacttcaggaagtatactgcgttcaccatacctagtataaacaatgaaacaccagggattaggtatcaatataatgtacttccacagggatggaaaggatcaccagcaatattccagagtagcatgataaaaatcttagagccctttagggcacaaaatccagaaatagtcatctatcaatatatggatgacttatatgtaggatctgacttagaaataggacaacatagagcaaaagtagaggagttaagagaacatttactaaggtggggattcaccacaccagataagaaacatcagaaagaacccccatttctttggatggggtatgaactccaccctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtaggaaaactaaattgggcaagtcagatttacccagggatcaaagtagggcaactttgtaaactccttaggggagccaaagcactaacagacatagtaccactaactgaagaagcagaattagaattggcagagaacagggagattctgagagaaccagtacatggagtatattatgacccatcaaaagatttgatagctgaaatacagaaacaggggcaagaccaatggacatatcaaatttaccaagaaccattcaaaaatctgaaaacaggaaagtatgcaaaaagg---aggacggcccacactaatgatgta------aaacagttaactgaggcagtgcgaaaaatagccatggaaagcatagtaatatggggaaag---actcctaaatttaggctacccatccaaaaaggcacatgggaaatatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtatcagctggagaaagagcccatggcaggagtagaaactttctatgtagatggagcagctaatagggaaactaaagtaggaaaagcagggtatgttactgacagaggaaggcagaaa---gttgttactctaactgaaacaacaaatcagaagactgaattacaagcaattcagctagctttgcaagattcaggatcagaag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+>C.ZA.04.04ZAPS195B1.DQ164118
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccctt-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgta-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----gactggtgagtacgcc----------------------aaattttatttgact----------agcaga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggggaaaaattagatacatgggaaaaaattacgtta---agg------cca---gggggacggaaacgctatatgctgaaacatctagtatgggcaagcagggagctggaaagatttgcacttaaccctggccctttagaaacatcagaaggctgtaaacaaatattgagacagctacaaccagct---cttcagacaggaacagaggaacttagatcattattcaacacagta---gccactctctattgtgtacataaaaagatagatgtacgcgacaccaaggaagccttagacgcaatagagaaagaacaaaacaaatgtcag------------------------caagaaacacagcagacagaaggg---------------------gctgacaga------------------------------aag------------------------gtcagtcaaaattatcctata------------gtacagaatcttcaagggcaaatggtacatcagaccctgtcacctagaactttgaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccacccccgcagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ctaaaagat---accatcaatgaggaggctgcagaatgggatagattgcat---ccagtacatgca---gggcctgttgcaccaggccaaatg---agagaacctaggggaagtgatatagcaggaacaactagtacc---ctacaggaacaaatagcatggatgaca---------agtaaccca---cct---gtc---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaagggccaaaggaaccctttagagactatgtggaccggttctttaaaactttaagagctgagcaagccacccaagatgtaaaaaattggatgacagagaccttgttggtccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccagcagcttcattagaagaaatgatgacagcatgtcagggagtgggaggacctagccacaaa---gcaagagtgttggctgag------gcaatg---agccaaacaaac---------------------------aatgccata---atgatg------cagagaagcaac---------ttt---aaaggccctagaaaa------attgttaaatgtttcaactgtggcagggaaggg---cacatagccagaaattgcagggcccctaggaaaaaaggctgctggaaatgtgggaaagaaggacaccaaatgaaagattgt---------------actgaaaggcaggctaattttttagggaaaatttggcc---ttccctcaa------ggg---gag---gccagggaatttccttcagaacagactagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccctgc------------------------------tccgaa---------------gcaggagcc------------gaaagacag---------------------------ggg------------------------acccttaactgccctcaaatcactctttggcggcgaccccttgtctcaataaaagtagggggccagataaaggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttattaaagtaagacagtat---gatcagatacctatagaaatttgtgggaaaaaggctataggtacagtattagtaggacctacacctgtcaac---ataattggaaggaatatgttgactcagcttggatgcacactaaattttccaattagtcccattgaaactataccagtaaaattaaagccaggaatggatggcccgagggttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagcaatttgcgaa------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaacccatataacactccagtatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagattttagggaactcaataaaagaacccaagacttttgggaa---gttcag------tta---ggaata---------------------------ccacacccagcagggttaaaaaggaaa---aaa------tcagtaacagtactggatgtaggggatgcatat---ttttcagttccgttagatgaaggcctcagaaaatatactgcattcaccatacctagtataaacaatgaaacaccagggattagatatcaatacaatgtgcttccacagggatggaaaggatcaccagcaatattccagtgtagcatgacaagaatcttagagccctttaggacacaaaatccagaaatagtcatctatcaatatatggatgacttatatgtaggatctgacctagaaataggacaacacagggcaaaaatagagaagttaagagagcatctgttaaagtggggatttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaagaa---agctgggctgtcaatgatatacagaagctagtgggaaaattaaactgggcaagtcagatttacccagggattaaagtaacgcaactttgtaaactccttaggggggccaaagcactaacagacatagtaccactaactgaagcagcagagttagaattagcagagaacagggaaattctaaaagaaccagtacacggagtatattatgacccatcaaaagatttgatagctgaactacagaagcaggggcatgaccaatggacatatcaaatttaccaagaatcattcaaaaatctgaaaacaggaaagtatgcaaaaagg---aggactgcccacactaatgatgta------aaacagttagcggaggcagtgcaaaaaatagccatggaaagcatagtaatatggggaaag---actcctaaatttagattacccatccaaaaggaaacatgggaaacctggtggacggactattggcaagccacatggattcctgattgggagtttgttaatacccctcctctagtaaaattgtggtaccagctggagaaagaacccatagcaggagtagaaactttttatgtagatggagcagctaatagagaaactaaaataggaaaagcagggtatgttactgacagaggaagacagaaa---attgtcactctaaatgaaacaacaaatcaaaagactgaattacaagcaattcagctagctttgcaagattcaggatcagaag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+>C.ZA.04.04ZAPS197MB1.DQ369997
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+>C.ZA.04.04ZAPS198MB1.DQ445637
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagatcaat-tttg-g-tcgtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------gcgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----gactggtgagtacgcc----------------------aatttttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattacgaggcgaaaaattagataaatgggaaagaattaggtta---agg------cca---gggggaaagaaacactatatgctaaaacatttagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacagcagaaggctgtaaacaaataatgaaccagctacatccagcc---cttcagacaggaacagaggaacttaaatcattattcaacacagta---gcaactatctactgtgtacatgcaaagatagaggtacgagacaccaaggaagccttagacaagatagaggaagaacaaaagaaaagtcag------------------------caaaaaacacagcaagcaaaagcg---------------------gctgacgga------------------------------caa------------------------gtcagtcaaaatcatcctata------------gtgcagaatcttcaagggcaaatggtacaccaagccttatcacctagaaccttgaatgcatgggtaaaagtgatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatctaaataccatgttaaatacagtggggggacatcaa---gcagccatgcagatg---ttaaaagat---accatcaatgaggaggctgcagaatgggataggttacat---ccagtacatgca---gggcctattgcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------agtaaccca---cct---att---ccagtg---ggagacatctataaaagatggataattatggggttaaataaaatagtgagaatgtatagccctgtcagcattttggacataagacaagggccaaaggaaccctttagagactatgtagatcggttctttaaaactttaagagctgaacaagctacacaagaggtaaaaaattggatgacagaaaccttgttagtccaaaatgcaaacccagattgtaagaccattttaagagcattaggaccaggggccacattagaagaaatgatgacagcatgtcagggagtgggaggacctagccacaaa---gcaagagtgctggctgag------gcaatg---agccaaacaaac---------------------------aacaacata---atgatg------cagaggggcaat---------ttt---aaaggctctaaaaga------attgtcaaatgtttcaactgtggcaaggaaggg---cacatagccaaaaactgcagggcccctaggaaaaaaggctgttggaagtgtgggaaagaaggacaccaaatgaaggattgt---------------aatgagagacaggctaattttttagggagaatttggcc---ttcccacaa------gggggggag---gccagggaacttccttcagagcaggccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggagcc------------gaaggacag---------------------------gga------------------------acccttaatttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggccagataagagaggctctcttagacacaggagcagatgatacagtatta---gaagac---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattgggggttttatcaaagtaagacagtat---gatcaaatagttatagaaatttgtgggaaaaaggctataggtacagtattagtgggacctacgcctgtcaac---ataattggaagaaatatgttgactcagcttggatgcacactaaattttccaattagtcccattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccactgacagaagag---aaaataaaagcattaacagcaatttgtgat------gaaatggagaaagaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagt------accaagtggaggaaattagtagacttcagggaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaatc---------------------------ccacacccagcaggattaaaaaagaaa---aaa------tcagtgacagtactagatgtaggggatgcatat---ttttcagttcctttagatgaagacttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccaggaattagatatcaacacaatgtgctcccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaaaatcttagagccctttagagcacaaaatccaggaatagtcatttatcaatatatggatgacttatatgtaggatctgacttagaaataggacaacatagagcaaaaatagaggagctaagagaacatctattaaagtggggatttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttatccaggaatcaaagtaaggcagctttgtaaactccttagggggactaaagccctaacagacatagtaaaactaactgaagaagcagaattagaattggcagagaacagggaaattctaaaagaaccagtacatggagtatattatgacccatcaaaagagctgatagctgaaatacagaaacaggggcaggatcaatggacatatcaaatttatcaagaaccattcaaaaatctgaaaacaggaaagtatgcaaaaagg---aggacggcccacactaatgatgta------agacagttaacagaagcagtgcaaaaaatagccttggaaagcatagtaatatggggaaag---actcctaaatttagactacccattcaaaaggaaacatgggaaacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagctggagaaagagcccatagtaggagcagaaactttctatgtagatggagcagctaatagagaaactaaaatgggaaaagcagggtatgttactgataaaggaaggcagaaa---gttgttactctaactgaaacaacaaatcagaagactgaattacaagcaattcacctagccttgcaagattcaggatcagaag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+>C.ZA.04.04ZAPS199B1.DQ164110
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccatt-tgtg-g-cagtgtggaaaa-tttctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagaa--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--gggc-----gactggtgagtacgcc----------------------aaattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggcgaaaaattagatagatgggaaagaattaggtta---agg------cca---gggggaaagaaacattatatgttaaaacacatagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacatcagaaggctgcaaacaattaatgacgcagctacaaccagct---cttcagacaggaacagaggaacttaaatcattatataacacagta---gcaaccctctattgtgtacatgaaaagatagatgtacgagacaccaaggaagccttagacaaaatagaggagaaacaaaacaaaagtcag------------------------caaaaaacacagcaagcacaagcg---------------------gctggcgga------------------------------cag------------------------gtcagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtacatcaacccttatcacctagaaccctaaatgcatgggtaaaagtaatagaggagaag------ggttttaacccagaggtaatacccatgtttacagcattatcagaaggagccactccacaagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaagaggctgcagaatgggatagattacat---ccagtacatgca---gggcctgttgcaccaggccaattg---agagaaccaaggggaagtgacatagcaggaactactagtaac---cttggggaacaaatagcatggatgaca---------aataaccca---cct---gtt---ccagtg---ggagacatctataaaagatggataattctgggtttaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaagggccaaaggaaccctttagagactatgtagatcggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgctggtccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccaggggcttcattagaagaaatgatgacagcatgtcaaggagtgggaggacctagccacaaa---gcaagagtgttggctgag------gcaatg---agccaagcaaac------------------------gggggaaatata---atgatg------cagagaagcaat---------ttt---aaaggctctaaaaga------attgttaaatgttttaactgtggcaaggagggg---cacatagccagaaattgcagagctcctaggaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagactgt---------------actgagagacaggctaattttttagggagaatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagaacagaccagagccaacagc------------------------------------------------------cccaccagc------agagatcttcgagtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggagcc------------gagagacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcaacgaccccttgtcacaataaaaatagggggccagacaaaggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaagccaaaaatgataggaggaattggaggttttatcaaagtaagacaatat---gatcaaatacttatagaaatttgtgggaaaaaggctataggtacagtattagtagggcctacacctgtcaac---ataattggaagaaacatgttgactcagcttgggtgcacactaaattttccaattagtcccattgaaactgtaccagtaaaattgaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagaa---aaaataagagcattaacagaaatttgtaaa------gaaatggagaaggaaggaaaaattaccaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttggggg---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtgacagtactggatgtgggggatgcatat---ttttcagttcctttagatgaagacttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccagggattagatatcaatataatgtgcttccacagggatggaaagggtcaccagcaatattccagagtagcatgacaaaaattttagagccctttagagcacaaaatccagaaatagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaagagttaagagaacatctgttaaagtggggatttaccacaccagacaagaaacatcagaaagaacccccatttctttggatgggatgtgaactccaccctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaattgggcaagtcagatttacccagggattaaagtaaagcaactttgtaaactccttaggggggccaaagcactaacagacatagtgctactaactgaagaagcagaattagaattggcagagaacagggaaattctaaaagaaccagtacatggggtatattatgacccatcaaaagacttgatagctgaaatacagaaacaagggtatgaccagtggacatatcaaatttaccaagaaccattcaaaaatctgaagacaggaaagtatgcaaaaagg---aggactgcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccacggaaagcatagtaatatgggggaag---actcctaaatttagattacccatccaaaaagaaacatgggaactatggtggacagactattggcaagccacctggattcctgagtgggaatttgttaatacccctcccctagtaaaattatggtaccagctggagaaagaacccgtagcaggagcagaaactttctatgtagatggagcagctactagggaaactaaaataggaaaagcagggtatgttactgacagaggaaggcagaaa---gttgtctctctaagtgaaacaacaaatcagaaggctgaattacaagcaattcagctagctttgcaagattcagggtcagaag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+>C.ZA.04.04ZAPS214B1.DQ093588
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+>C.ZA.04.04ZASK031B2.AY901974
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+>C.ZA.04.04ZASK131B1.DQ056412
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+>C.ZA.04.04ZASK132B1.DQ093594
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagacca-a-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ccgaaagcgaaag------------------------------------------taagaccagagaa--------gttcgctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----gactggtgagtacgcc----------------------aaattttatttgact----------agcgga-gg---------ctagg-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagagggggaaaattagataaatgggaaaaaattagttta---agg------cca---gggggaaagaaacgctatatgctaaaacacttagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagagacatcagaaggctgtaaacagataatgaaacagctccaaccagct---attcagacaggaacagaggaacttaaatcattatataacacagta---gcaactctctattgtgtacatgaaggcatagaggtacgagacaccaaggaagccttagacaaaatagaggaagaacaaaacaaatgtcag------------------------cagaacacacagcaggcaaaagcg---------------------gctgacgga------------------------------aaa------------------------gtcagtcaaaattatcctata------------gtgcagaatatccaagggcaaatggtacaccaggccatatcacccaggactttgaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaggtaatacccatgttttcagcattatcagaaggagccaccccaacagatttaaacaccacgttaaatacagtggggggacatcaa---gcagccatgcagatg---ttaaaagat---accatcaatgaggaggctgcagaatgggatagactacat---ccagtccatgca---gggcctattgcaccaggacaactg---agggagcctaggggaagtgacatagcaggaaccactagtacc---cttcaggaacaaatagcatggatgacg---------aataaccca---cct---gtc---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgttagcattttggacataaaacaggggccaaaagaaccctttagagattatgtagaccggttctttaaatgtttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcaaacccagattgtaagaccattctaagagcattaggatcaggggctaccttagaagaaatgatgacagcatgccagggagtgggaggacctagccacaaa---gtaagagtattggctgag------gcaatg---agccaagcaaac---------------------------agtaacata---ctgatg------caaagaagcaat---------ttt---aaaggatctaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccagaaattgcagggcccctagaaaaaaaggatgttggaaatgtggaaaagaaggacaccaaatgaaagactgt---------------actgagaggcaggctaattttttagggaaaatttggcc---ttccaacaa------ggg---gag---gccagggaatttccttcagagcagaccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccccac------------------------------tccgaa---------------gcaggagcc------------gagaggcag---------------------------gga------------------------acccttaatttccctcaaatcactctttggcaacgaccccttgtcacaataaaagtagggggccagacaaaggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaaaggctataggtacagtattagtagggcctacacctgtcaac---ataattggaagaaacatgttgactcaacttggatgcacactaaattttccaattagtcctattgaaactgtaccagtaaaactgaagccaggaatggatggcccaagggttaaacaa---tggccattgacagaagaa---aaaataaaggcattaacagcaatttgcgaa------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacacgccaatatttgctataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaggacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcaggattaaaaaagaaa---aaa------tcagtgacagtactggatgtgggggatgcatat---ttttcagttcccttagataaaaacttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccagggattagatatcaatataatgtgcttccacaagggtggaaggggtcaccagcaatattccagagtagcatgacaagaatcttagagccctttagagcacaaaacccagaaatagtcatctatcaatatatggatgacttatatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaggagttaagagaacatttattaaggcggggattcaccacaccagataagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgataaatggacagtacagcctataaagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacgcagggattaaagtaaggcaactttgtaaactccttaggggggccaaagcattaacagacatagtaccactaactgaagaagcagaattagaattagcagagaacagggaaattctaagagaaccagtacatggagtatattatgacccatcaaaagatttgatagctgaaatacagaaacaggggcatgaccaatggacatatcaaatttaccaagaaccattcaaaaatctgaaaacagggaagtatgcaaaaagg---aggacggcccacactaatgatgta------aaacagctaacggaggcagtgcaaaaaatagccatggaaagtatagtaatatggggaaag---actcctaagtttagactacccatccaaaaagaaacatgggaaacatggtgggcagactactggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtatcagctggagaaagaacccatggcaggaatagaaactttctatgtagatggagcagctaatagggaaactaaaataggaaaagcagggtatgttactgatagaggaaggcagaaa---gttgttactacaactgaaacaacaaatcagaaggctgaactactagcaattcagctagctttgcaagattcaggatcagaag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+>C.ZA.04.04ZASK135B1.DQ011166
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+>C.ZA.04.04ZASK147B1.DQ164114
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+>C.ZA.04.04ZASK148B1.DQ093590
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+>C.ZA.04.04ZASK150B1.DQ011178
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagactcct-tttg-g-tagtgtgaaaaa-tctctagcagtggcg--------cccgaacagggac------------------ctgaaagcgaaag------------------------------------------taagaccagagaa--------gatctctcgacgca-ggactcggcttgct--gaaagtgcactcggcaagaggc-------------gagggga--aggc-----ggctggtgagtacgcc-----------------------aattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaaaagggggaaaattagatacatgggaaaaaattaggtta---agg------cca---gggggaaagaaacgctataggataaaacacctagtatgggcaagcagagagctggaaagatttgcacttaaccctggccttttagagacatcagacggctgtaaacaaataatacaacagctacaaccagct---cttcaaacaggaacagaggaacttagatcattattcaacacagtg---gcaactctctattgtgtacataaaaagatagatgtaagagacaccaaggaagccctagacaagatagaggaagaacaaaccaaaagtcag------------------------caaaaaacacagcaggcagaaatg---------------------gctgctgga------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatctacaagggcaaatggtacatcaacccatatcacctagaactttgaatgcatgggtaaaagtaatagaggagaag------ggttttaaccccgaggtaatacccatgttttcagcattatcagagggagccaccccacaagatttaaacaccatgttaaatacaattgggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaagaggctgcagaatgggatagattacat---ccagtacatgcg---gggcctattgcaccaggccaaatg---agagaaccaaggggaagtgatatagcaggaactactagtacc---cttcaggaacaaataggatggatgaca---------cataaccca---cct---att---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataagacaagggccaaaggaaccctttagagactatgtagatcggttctttaaaactttaagagctgaacaagctacacaagatgtaaagaattggatgacagagaccctgttggtccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccacaggctacattagaagaaatgatgacagcatgccagggagtggggggacctggccacaaa---gcaagagtgttggctgag------gcaacg---agccaagcaaac------------------------agtatgaatatg------atg------cagagaagcaat---------ttc---aagggccctagaaga------attattaaatgtttcaactgtggcaaggaagga---cacatagccaaaaactgcagggcccctaggaaaaaaggctgttggaaatgtggaaaggaagggcaccaaatgaaagactgt---------------actgagaggcaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaattttctccagaacagaacagagccaacagc---------------------------------cccaccagcagagccaacagccccaccagc------agagagcttcaagtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggagcc------------gaaagacag---------------------------gga------------------------acccttaatttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggacagacaaaggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaagatggaaaccaaaaatgataggaggaattggaggttctatcaaagtaagacaatat---gatcaaatagtaatagaaatctgtggtaagaaggctataggtacagtattagtaggacctacgcctgtcaac---ataattggaagaaatatgttgactcagcttggctgcactctaaattttccaattagtcccattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacagaaatttgtact------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataatactccagtatttgccataaaaaagaaagacagt------actaaatggagaaaattagtagatttcagggaacttaataaaagaactcaagacttttgggaa---gttcaa------tta---ggaata---------------------------ccacatccagcagggttaaaaaagaaa---aaa------tcagtgacagtactggatgtgggggatgcatat---ttttcggttcctttagatgaaagcttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccagggatcagacatcaatataatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaagaatcttagagccctttagagcaaaaaatccagaaatagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaggagttaagagaacatctattaaagtgggggtttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgagctccatcctgacaaatggacagtacaacctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttaccgagggattaaagtaaggcaactttgtaaactccttaggggggccaaagcactaacagacatagtaccactgactgaagaagctgagttagaattagcagagaacagggagattctaaaagagccagtacatggggtatattatgacccatcaaaagacttgatagctgaagtacagaaacagggacatgatcaatggacatatcaaatttaccaagaaccattcaaaaatctaaaaacaggaaaatatgcaaaaatg---agaactgcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccttggaaagtatagtaatatggggaaag---actcctaagtttagactacccatccaaaaagaaacatgggagacatggtggacagattattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagctggagaaagaacccatagcaggagtagaaactttctatgtagatggagcagctaatagggaaactaaaataggaaaagcagggtatgttactgacagaggaaggcagaaa---gttgtttgtctaaatgaaacaacaaatcagaagactgaattacaagcaattcagctagctttgcaagattcaggatcagaag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+>C.ZA.04.04ZASK151B1.AY901977
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+>C.ZA.04.04ZASK154B1.AY878071
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+>C.ZA.04.04ZASK155B1.AY901978
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+>C.ZA.04.04ZASK156B1.DQ011171
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+>C.ZA.04.04ZASK160B1.DQ011173
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+>C.ZA.04.04ZASK164B1.DQ056405
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+>C.ZA.04.04ZASK165B1.DQ396387
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagacca-t-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taggaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--gggc-----ggctggtgagtacgcc----------------------aaatttttcttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatcttaagagggggaaaattggatacatgggaacaaattaagtta---agg------cca---gggggaaagaaaaggtatatgataaaacacctagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacagcaaagggatgcaaacaaataataagccagcttcaaccagct---ctgcagacaggaacagaggaacttagatcattatacaacacagta---gcaactctctattgtgtacatgcagggataaaggtacgagacaccaaggaagccctagataagatagaggaggaacaaaacaaatgtcag------------------------caaaaaacgcagcaggcagaagca---------------------gctgctgaa------------------------------aag------------------------accagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtacaccaggccatatcacctagaactttgaatgcatgggtaaaggtaatagaggagaag------ggcttcaaccccgaggtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaggaggctgcagaatgggatagattacat---ccagtacctgca---gggcctgttgcaccaggccaaatg---agagacccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcgtggatgaca---------aacaaccca---cct---gtt---cccgtg---ggagacatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggatataaaacaagggccaaaggaaccctttagagactatgtagatcggttctttaaaactttaagagctgaacaagctacacaagatgtaaagaattggatgacagacaccttgttgatccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccaggggctacattagaagaaatgatgacagcatgtcagggagtgggaggacccagccacaaa---gcaagagtgttggctgag------gcaatg---agccaagcacaa------------------------aatgcaaatata---atgatg------cagaaaagcaat---------ttc---aaaggtcctagaaga------attattaaatgtttcaactgtggcaaggaaggg---cacatagccaaaaattgcagggcccctagaaaaaagggttgttggaaatgtggaaaggaaggacaccaaatgaaagactgt---------------atcgagagacaggctaattttttagggaaaatctggcc---ttcccacaa------ggg---gag---gccagggaatttcctgcagaacaggccagagccaacagc------------------------------------cccaccagagccaacagctccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggagct------------gaaaggcgg---------------------------gga------------------------acacttaactgccctcaaatcactctttggcagcgacctcttgtctcaataaaagtagggggccagataaaggaagctctcttagacacaggagcagatgatacagtatta---gaagaa---ataagtttaccaggaaaatggaaaccaaaaatgataggaggaattggaggctttattaaagtaagacagtat---gatcaaatacctatagaaatttgtggaaaaaaggctataggtacagtattagtaggacctacacctgtcaac---ataattggaaggaatctgttgactcagcttggctgcactctaaattttccaatcagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagaaatctgtaca------gaaatggaaaaggaaggaaaaatttccaaa---attgggcct---gaaaatccatataatactccagtatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtaacagtattggatgtaggggatgcatat---ttttcagttccgttagatgaaaacttcaggaaatacactgcattcaccatacctagtataaacaatgagacaccagggattagatatcaatataatgtgcttccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaaaatcttagagccctttagggcacaaaatccagacatagtcatctatcaatatatggatgatttgtatgtaggatctgatttagaaatagggcaacatagagcaaaaatagaggaattaagagaccacctattaaagtggggattcaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgataaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatctatgcagggattaaagtgaggcaactatgtaaactccttagggggaccaaagcactaacagacatagtaccactgactgaagaagcagaattagaattggcagagaacagggaaattttaaaagaaccagtacatggagtatattatgacccagcaaaagacttgatagctgaaatacagaaacaaggacatgatcaatggacatatcaaatttaccaagaaccattcaaaaatttaaaaacaggaaagtatgcaaaaatg---cggactgcccacactaatgatgta------aaacagttaacagaggcagtgcagaaaatagccatggaaagtatagtaatatggggaaag---actcctaaatttagactacccatccaaaaggaaacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagttggaaaaagatcccatggttggagtagaaactttctatgtagatggagcagctaatagggaaactaaagcaggaaaagcagggtatgttactgacagaggaaggcaaaaa---gttatttctctaactgaaacaacaaatcagaagactgaattacaagcaatcctgctagctttgcaagattcaggatcagaag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+>C.ZA.04.04ZASK170B1.DQ093595
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+>C.ZA.04.04ZASK171B1.DQ351217
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------tctagagatc-------cctcagaccaac-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc----------------------aaattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagcgcgtcaatattacaaggcgaaaaattaggtaaatgggaaaaaattagatta---agg------cca---gggggaaagaaaagatataggctaaaacacctagtatgggcaagcagggagctggaaagatttgcacttaaccctggtcttttagaaacatcagaaggctgtaaacaaataatacaacagctacaaccagct---cttaagacaggaacagaggaacttaaatcattatacaacacagta---gcaactctctattgtgtacatggaaagatagaggtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaagtcag------------caaaaaacacagcaaaaaacacagcaggcagaagcg---------------------gctggcgga------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtacaccaggccctatcacctagaactttgaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccagcagatctaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaggaggctgcagaatgggataggatgcat---ccagtacatgca---gggcctattgcaccaggccaaatg---agagaaccaaggggaagtgacatagcagggactactagtacc---cttcaggaacaaatagcatggatgaca---------agtaaccca---cct---gtc---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaggggccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccctgttggtccaaaatgcaaacccagattgtaagaccattttaagagcattaggaccaggggctacattagaagaaatgatgacagcatgtcagggagtgggaggacctagccacaaa---gcaagagtgttggctgag------gcaatg---agccaagcaaat------------------------ggtacaaacata---atgata------cagagaaacaat---------ttt---aaaggctctaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccagaaattgcagggcccctaggaaaaaaggctgttggaaatgtgggagagaaggacaccaaatgaaagactgt---------------actgagaggcaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagaacagaccagagccaatagc---------------------------ccctcagaacaggctagagccaacagccccaccagc------agagagcttcaggtt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------gcaggaggc------------gaaagacag---------------------------gga------------------------acccttaatttccctcaaatcactctttggcagcgaccccttgtcacaataaaagtagggggtcaagtaaaggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccagggaaatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaaaggctataggtacagtattagtagggcctacacctgtcaac---ataattggaagaaacctgttgactcagcttggatgcacactaaatttcccaattagccctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagcaatttgtgaa------gaaatggaaaaggaagggaaaattacaaaa---attgggcct---gaaaatccatataacactccagtatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggagctcaataaaagaactcaagacttttgggag---gttcaa------tta---gggata---------------------------ccacacccagcagggttaaaaaagaga---aaa------tcagtgacagtactggatgtgggggatgcatat---ttttcagttcctttagatgaaggcttcaggaaatatactgcatttaccatacctagtgtaaacaatgaaacaccagggattagatatcaatataatgtgcttccacagggatggaaggggtcaccagcaatattccagtgtagcatgataaaaatcttggagccctttagagcacaaaatccagaaatagtcatctatcaatatatggatgacttatatgtaggatctgacttggaaatagggcaacatagagcaaaaatagaggagttaagagaacatctgttaaaatggggattcaccacaccagataagaaacatcagaaagaacccccatttctctggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttatgcagggattaaggtaaggcaactttgtaaactccttaggggggccaaagcattaacagacatagtaccactaactgaagaagcagaattagaattagcagaaaacagggaaattttaagagaaccagtacatggagtatattatgacccatcaaaagacttaatagctgaaatacagaaacaggggtgtgaccaatggacatatcaaatttaccaggaaccattcaaaaatctgaaaacagggaagtatgcaaaaatg---ggaaccgcccacactaatgatgta------aaacagttaacagaggcagtgcagaaaatagccttggaaagcatagtaatatggggaaag---actcctaaatttagactacccatccagaaagaaacatgggagagatggtggacagactattggcaggccacctggattcctgagtgggagtttgttaataccccccccctagtgaaattatggtaccagctggaaaaagaacccatagcaggagcagaaactttctatgtagatggagcggctaatagggaaactaaactaggaaaagcagggtatgttactgacagaggaaggcagaaa---attgtttctctaaatgaaacaacaaatcagaaggctgagttacaagcaattcagctagctttgcaggattcaggatcagaag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+>C.ZA.04.04ZASK173B1.DQ093604
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+>C.ZA.04.04ZASK174B1.AY901980
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+>C.ZA.04.04ZASK176B1.DQ056416
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+>C.ZA.04.04ZASK178B1.DQ093587
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+>C.ZA.04.04ZASK180B1.AY878059
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+>C.ZA.04.04ZASK193B1.DQ396396
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+>C.ZA.04.04ZASK202B1.DQ011180
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actggagatc-------cctcagaccctt-tttg-g-ttgtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ctgaaagtgaaag------------------------------------------taagaccagagaa--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc-----------------------taatttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagagggggaaaattagatacatgggaaagaattaagcta---agg------cca---gggggaaagaaatgctatatgctaaaacacatagtatgggcaagcagagagctggaaagattcgcacttaaccctggccttttagaaacatcggaaggctgtaaacaaataatgcaacagctacaaccagct---cttcagacaggaacagaggaacttaaatcattattcaacacagta---gcagttctctattgtgtacataaaaagatagaggtacaagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaagtcag------------------------caaaaaacacagcaggcagaagcg---------------------gctggcggg------------------------------aaa------------------------gtcagtcaaaattatcctata------------gtgcagaatgcccaagggcaaatggtgcaccaggccatatcacctaggactttgaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccaccccacaagacttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgatgaggctgcagaatgggatagagtacat---ccagtacaggca---gggcctattgcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacagatagcatggatgaca---------ggtaaccca---cct---atc---ccagta---ggagacatctataaaagatggataattttagggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaagggccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagggctgaacaagctacacaagatgtaaaaaactggatgacagacaccttgttggtccaaaatgcaaacccagattgtaagaccattttaagggcattaggaccagcggcctcattagaagaaatgatgacagcatgtcagggagtgggaggacctggccataaa---gcaagagtgctagctgaa------gcaatg---agccaagccaat------------------------aatacaaacata---atgatg------cagagaagcaat---------ttt---aagggccctaagaga------actgttaaatgtttcaactgtggcagggaaggg---cacatagccagaaattgcagggcccctagaagaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagaatgc------------actactgaaaggcaggctaattttttagggaaaatttggcc---ttccctcaa------ggg---aag---gccagggaatttcctacagaacagaccagagccaacagc------------------------------------cccactagagccaacagccccaccagc------agagagcttcaggtt------------cgagaa---gac---aac---ctctgc------------------------------gccgaa---------------gcaggagct------------gaacgacag---------------------------gga------------------------acccttaacttccctcaaatcactctttggcagcgaccccttgtctcaataaaagtagggggacagacaagggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacctatagaaatttgtggaaaaaaggctataggtacagtgttaatagggcctacacctgtcaac---ataattggaaggaatatgttgactcagcttggatgcacactaaattttccaattagtcccattgacactgtaccagtaaaattaaagccaggaatggatggcccaaaggtcaaacaa---tggccattgacagaagag---aaaataaaagcattaaaggcaatttgtgaa------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccagtatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagagaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtgacagtactagatgtgggggatgcatat---ttttcagttcctttagatgaagacttccgaaaatatactgcatttaccatacctagtataaacaatgagacaccagggattagatatcaatataatgtgctgccacagggatggaaaggatcaccggcaatattccagagtagcatgacaaaaatcttggagccctttagagcaaaaaatccagaaatagtcatctatcaatatatggatgacttgtatgtaggatctgacctagaaatagggcaacatagagcaaaaatagaagaattaagagaacatctattaaagtggggatttaccacaccagacaaaaaacatcagaaagaacccccatttctgtggatggggtatgaacttcatcctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatgtacagaagttagtgggaaaattaaattgggcaagtcagatttacccagggattaaagtgaagcaactttgcaaactccttagggggaccaaggcactaacaggcatagtaccactaactgaagaagcagaattagaattggcagagaacagggaaattctaaaagaaccagtacatggagtatattatgacccatcaaaagacttgatagctgaaatacagaaacaggggcttgaccaatggacatatcaaatttaccaagaaccattcaaaaatctgaaaacagggaagtatgcaaaaatg---aggactgcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccatggaaagcataataatatggggaaag---actcctaaatttagactacccatccaaaaagaaacatgggatatatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagctggagaaagaacccataataggggcagaaactttctatgtagatggagcagctaatagagaaactaaaataggaaaagcaggatatgttactgacagaggaaggcaaaaa---attgttgctctaagtgaaacaacaaatcagaggactgaattacaagcaattcatctagctttgcaagattcaggatcagaag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+>C.ZA.04.04ZASK204B1.DQ056414
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccaat-tgtg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-agactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc----------------------aaattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattacgaggggaacaattagatgcatgggaaaaaattaggtta---agg------cca---gggggaaagaaatgctatatgctaaaacacttagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacaacagaaggctgtaaacaaataatgcaacagctgcaaccagct---cttcagacaggaacagaggaacttagatcattatataacacagta---gccactctctattgtgtacataataagattgagatacgagataccaaagaagctttagacaagatagaggaagaacaaaacaaaagtcag------------------------caaaaaacacagcaggcaaaagcg---------------------gctgacgga------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtacaccaggccatatcaccgagaactttaaatgcatgggtaaaagtaatagaagagaag------gcttttagtccagagataatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacggtggggggacatcaa---gcagccatgcaaatg---ttaaaagaa---actatcaatgacgaggctgcagaatgggataggttacat---ccagtgcatgca---gggcctattgccccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------agtaaccca---cct---att---ccagtg---ggagacatctataaaagatggataattctggggttggataaaatagtgagaatgtatagccctgtcagcattttggacataaggcaagggccaaaggaaccctttagagactatgtagatcggttctttaaaaccttaagagctgaacaagctacacaagaagtaaaaaactggatgacagacaccttgttggtccaaaatgcaaacccagattgtaaaaccattttaagagcattaggaccaggggccacattagaagaaatgatgacagcatgtcagggagtgggaggacctggccacaaa---gcaagagtgttggctgag------gcaatg---agccaagtaaac------------------------catggaaacata---ctaatg------cagaaaagcaat---------ttt---aaaggctctaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccagaaactgtagggcccctaggaaaaaaggctgttggaaatgtggaaaggaaggacaccaaatgaaagactgt---------------actgagaggcaggccaattttttagggggaatttggcc---ttcccacaa------ggg---gag---gccagggaatttccttcagaacagaccagagccaacagc------------------------------------------------------cccaccagc------agagagcttcaggtt------------cgagga---------aac---ccccac------------------------------tccgaa---------------gcaggagct------------gaaagacag---------------------------gga---------------gtc------acacttaacttccctcaaatcactctttggcaacgaccccttgtctcaataaaaatagggggtcaggtaaaagaggctctcttagacacaggagcagatgatacagtatta---gaagac---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacaatat---gatcaaatacttatagaaatttgtggaaaagaggctataggtacagtattagtagggcctacacctgtcaac---ataattggaagaaatatgttgactcagcttggatgcacactaaattttccaattagtcccattgaaactgtaccagtaaaactaaagccaggaatggatggtccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacagcaatctgtgaa------gaaatggaaaaggaaggaaaaattacaaaa---attggacct---gaaaatccatataacactccagtatttgctataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtgacagtactggacgtgggggatgcatat---ttttcagttcctttagatgaaggcttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccagggattagatatcaatataatgtgctcccacagggatggaaaggatcaccagcgatattccaaagtagcatgacaaaaatcttagagccctttagagcaaacaatccagaaatagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagggcaacatagagcaaaaatagaggagttaagaaatcatctattaaggtggggattcaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttatgcagggattcaagtaaagcaactgtgcaaactccttaggggagccaaagcactaacagacatagtacaactggctgaagaagcagaattagaactagcagagaacagggaaattctaaaagaaccagtacatggagtatattatgaccccactaaagacttaatagctgaattacagaaacaggggcagagccaatggacatatcaaatttaccaagaaccattcaaaaatctgaaaacaggaaagtatgcaaaaatg---aggactgcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccttggaaagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaagaaacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggaatttattaatacccctccactagtaaaattatggtaccagttggagaaagaacccatagcagaggcagaaactttctatgtagatggagcagccaatagggatactaagatggggaaagcagggtatgttactgacaaaggaaggcagaag---gttgtgactctaactgaaacaacaaatcagaaggctgagttacaagcaattcagctagctttgcaggattcaggattagagg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+>C.ZA.04.04ZASK206B1.DQ056415
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg---tgtgactctggtaatact---ctggt-a---------------actagagatc-------cctcagaccc-t-agtg-g-tattgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taaaaccagagaa--------gatctctcgacgca-ggactcggcttgct---gaagtgcacgcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc-----------------------aattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggcgaaaagttagatagatgggaaaaaattaggtta---agg------cca---ggaggaaggaaacgttatatgataaaacacttaatatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacattagaaggctgtagacaaataataaaacagctacaaccagct---cttcagacaggaacagaggaacttagatcattatacaacacagta---gcaactctctattgtgtacatagcaatatagagataaaagacaccaaggaagccctagacaaaatagaggaagaacaaaacaaatgtcag---------------cagcaggcagaaaagcagcagcaggcagaaaag------------------gctgacaagagg---------------------------------------------------------gtcagtcaaaattatcctata------------gtgcagaatcttcaagggcaaatggtacaccaggccttatcacctagaactttgaatgcatgggtaaaagtaatagaggagaag------gcttttagcccagaagtaatacccatgtttacagcattatcagaaggagccacccccactgacttaaataccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagac---accatcaatgaggaggcggcagaatgggatagattacat---ccagcacaggca---gggccttatccagcaggccaaata---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaataacatggatgaca---------ggtaaccca---cct---att---ccagtg---ggagaaatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataaaacaagggccaaaggaaccttttagagattatgtagaccggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccaggggcctcattagaagaaatgatgacagcatgtcagggagtgggaggacctagccacaaa---gcaagagtattggctgag------gcaatg---agccaaacaaac---------------------------agtaccatc---atgatg------cagaaaagcaat---------ttt---aagggccctagaaga------aatgttaaatgtttcaactgtggcaaggaaggg---catgtagccagaaattgcagggcccctaggaaaaaaggctgttggaaatgtggaaaagagggacaccaaatgaaagattgt---------------actgaaagacaggttaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttcccccagagcagactagagccaacagc------------------------------------------------------cccaccagc------agagagcttcagggt------------cgagga---gac---aac---ccccgc------------------------------tccgaa---------------acaggagac------------gaaagacag---------------------------gga------------------------acccttaatttccctcaaatcactctttggcaacgaccccttgtctcaataaaagtagggggccagataaaggaggctcttttagacacaggagcagatgatacagtatta---gaagac---ataaatttgccaggaaattggaaaccaaaaatgataggaggaattggagggtttatcaaagtaagacagtat---gatcaaatacttatagaaatttgtggaaaaagggctataggtacagtattggttgggcctacacctgtcaac---ataattggaagaaatatgttgactcagcttggatgcacactaaattttccaattagtcctattgaaactgtgccagtgaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacagcaatttgtgaa------gacatggaaaaggaaggaaaaatcacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaacttaataaaagaactcaagatttttgggaa---gttcaa------tta---ggaata---------------------------cctcacccagcagggttaaaaaagaac---aaa------tcagtgacagtactggatgtaggggatgcatat---ttttcagtgcctttagatgaaggcttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccagggattagatatcaatataatgtgcttccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaaaatcttagagcccttcagggcacaaaatccagaaatagtcatatatcaatatatggatgacttgtatgtaggatctgatttagaaatagggcaacatagagcaaaaatagaggagttaagaaatcatctattaaaatggggatttaccacaccagacaagaaacatcagaaagaacccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacaactgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaactaaactgggcaagtcagatttacccagggattaaagtaaagcaactttgcaaactccttaggggggccaaagcactaacagacatagtaccactaactgaagaagcagaattagaattggcagagaacagggaaattataaaagaaccagtacatggggcatattatgacccgtcaaaagacttaatagctgaaatacagaaacaggggcatgaccaatggacatatcaaatttaccaagagccatttaagaacctgaaaacaggaaagtatgcaaaaatg---aggactgcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccatggaaagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaagaaacgtgggagacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatactcctcccctagtaaaattgtggtatcagttggagaaagaacccatagcaggagtagaaactttctatgtagatggagcagctagtagggagactaaaatgggaaaagcagggtatgttactgacagaggaaggcagaaa---attgttactctaaatgaaacaacaaatcagaaagctgaattgcaagcagttcagctagctttgcaagattcaggatcagaag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+>C.ZA.04.04ZASK208B1.DQ056406
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+>C.ZA.04.04ZASK217B1.DQ056417
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+>C.ZA.04.04ZASK234B1.DQ093605
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+>C.ZA.04.CAP61_8w_F3.GQ999975
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+>C.ZA.04.SK134B1.AY703909
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+>C.ZA.04.SK140B1.AY901973
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+>C.ZA.04.SK144B1.AY703911
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+>C.ZA.05.05ZASK243B1.DQ396372
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+>C.ZA.05.05ZASK244B1.DQ369992
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtggct---ctggt-a---------------actagagatc-------cctcagac-cat-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------taagaccagagaa--------gatctctcgacgca-agactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc-----------------------tattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaaaaggcgaaaatttagatagatgggaaagaattaggtta---agg------cca---gggggaaagaaacaatataggctaaaacacttagtatgggcaagcagggagctggaaagatttgcacttaaccctggtcttttagaaacatcagaaggctgtaaacagataataacacagctacaaccagct---cttcagacaggaacagaggaaattaaatcattatacaacacagta---gcagttctctattgtgtacttaaaaagatagaggtacgagacaccaaggaggccttagacaaaatagaggaagaacaaaaaacaagtcag------------------------caaaaagtacagcaggcaaaagcg---------------------gctgacgga------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtacatcagcccctatcacctaggaccttgaatgcatgggtaaaagtaatagaggaaaag------gcttttagcccagaggtgatacccatgtttacagcactatcagaaggagccaccccacaagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcagatg---ttaaaagat---accatcaatgaagaggctgcagaatgggatagattacat---ccagtccatgca---gggcctattgcaccaggccaaatg---agagaaccaaggggatgtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------agtaaccca---cct---att---ccagtg---ggggacatctataaaagatggataattctgggtttaaataaaatagtgagaatgtatagccctgtcagcattttggacataagacaaggaccaaaggaaccttttagagattatgtagatcggttctttaaagttttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaacccagattgtaagaccattttaagagcattaggaccggcagctacattagaagaaatgatgacagcatgtcaaggagtgggaggacctggccacaaa---gcaagagtgttggctgag------gcaatg---agccaagcaaac---------------------------agtaacata---atgatg------cagagaggtaat---------ttt---aaaggacctagaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacatagccaagaactgcagggcccctaggaaaaagggctgttggaaatgtggaaaggaaggacaccaaatgaaagactgt---------------actgagagacaggctaattttttagggaaaatctggcc---ttccaacaa------ggg---aag---gccagggaatttccatcagagcagactagaaccaacagc------------------------------------------------------cccaccagc------agagagcttcaagtt------------cgagga---gac---aac---ccctgc------------------------------tccgaa---------------gcaggagcc------------gaaagacag---------------------------gga------------------------acctttaacttccctcagatcactctttggcagcgaccccttgtctcaataaaaatagggggtcaggtaaaggaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gatcaaatacagatagaaatttgtggaaaaaaggctataggttcagtattagtagggcctacacctgtcaac---ataattggaagaaacatgttgactcagcttggatgcacactaaattttccaattagtcccattgaaactataccagtaaaactaaagccaggaatggatggcccaaaggttaaacaa---tggcccttaacagaagaa---aaaataaaagcattaacagcaatttgtgaa------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataatactccaatatttgccataaaaaaggaggacagt------acaaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcatggttaaaaaagaaa---aaa------tcagtgacagtactggatgtgggggatgcatat---ttttcggttcctttagatgaaggcttcaggaaatatactgcattcaccatacccagtgtaaacaatgaaacaccagggattagatatcaatataatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatcttagagccctttagagcaaaaaatccagaaatagtcatctatcaatatatggatgacttatatgtaggatctgatttagaaatagggcaacacagagcaaaaatagaggagttaagagaacatctattaaagtgggggtttaccacaccagacaagaaacatcaaaaagaaccccctttcctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagac---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattgaactgggcaagccagatttacccaggaataaaagtaacacagctttgtaaactccttaggggggccaaagcactaacagacatagtaccactaactgaagaagcagagttagaattagcagagaacagggaaattctaaaagaaccagtacatggagtatattatgacccatcaaaagacttaatagctgaaatacagaaacaggggtgtgaccaatggacatatcaaatttaccaagaaccatttaaaaatctgaaaacagggaagtatgcaaaaagg---aggacggcccacactaatgatgta------aaacagttaacagaggcagtgcaaaaaatagccatggaaagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaagaaacatgggaaatatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatacccctcccctagtaaaattatggtaccagctggagaaagaccccatagcaggagcagaaactttctatgtagatggagcagctaatagggaaactaaaataggaaaagcagggtatgttactgacaaaggaaggcagaaa---attgttaccctaagtgaaacaacaaatcagaagactgaattacaagcaattcagctagctctgcaagattcaggatcagaag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+>C.ZA.05.05ZASK246B1.DQ369983
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctg-t-tg--------------tgtggct---ctggt-a---------------actagagatc-------cctcagaccctt-tttg-g-tagtgtggaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag------------------------------------------tcagaccagagga--------gatctctcgacgca-agactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc----------------------aaattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggcgaaaaattagatagatgggaaagaattagattg---agg------cca---gggggaaagaaacactatatgttaaaacacctaatatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagaaacatcagaaggctgtaaacaaataatgacacagctacacccagct---cttcagacaggaacagaggaacttaaatcattatacaacacagta---gcaactctctattgtgtacatgaaaagatagaggtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaaaggcag------------------------caaaaaacacagcaggcaaaagcg---------------------gctgacggg------------------------------aaa------------------------gtcagtcaaaattatcccgta------------gtgcagaatctccaagggcaatgggtacatcaagccataacacctagaactttgaatgcatgggtaaaggtagtagaggagaag------gcttttagcccagaggtaatacccatgttttcagcactatcagaaggagccaccccatcagatttaaacagcatgttaaatacggtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaagaggctgcagaatgggatagaacacat---ccagtacatgca---gggcctattgcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtacc---cttcaggaacaaatagcatggatgaca---------agtaaccca---cct---att---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtgagaatgtatagccctaccagcattctggacataagacaagggccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagagctgaacaagctacacaagaggtaaaaaattggatgacagataccttgttggtccaaaatgcaaacccagattgtaagaccattttaaaagcattaggatcaggggcctcaatagaagaaatgatgacagcatgtcagggagtgggaggacctggccacaaa---gcaagagtgttagctgag------gcaatg---agccaggcaaac------------------------aatataaacata---atgatg------cagagaaacaat---------ttt---aaaggccctagaaga------attgttaaatgttttaattgtggcaaggaaggg---cacatagccaaaaactgcagggcccctaggaaaaagggctgttggaaatgtggaaaggaaggacaccagatgaaagactgt---------------actgagaggcaggctaattttttagggaaaatttggcc---ttcccagaa------ggg---gag---gccagggaatttccttcagaacagaccagagccaacagc------------------------------------cccaccagcgccaacagccccaccagc------agagagcttcaggtt------------cgagga---ggc---aac---ccccgc------------------------------gccgaa---------------gcaggacca------------gaaagacag---------------------------gga------------------------acctttaacttccctcagatcactctttggcagcgaccccttgtctcaataaaagtagggggtcaggtaaaagaggctctcttagacacaggagcagatgatacagtatta---gaagac---ataaatttgccaggaaaatggaaaccaaaaatgataggtggaattggaggttttatcaaagtaagacaatat---gaccaaatacctatagaaatttgtggaaaaaaggctataggttcagtattagtagggcctacacctgtcaac---ataattgggaggaatatgtcgactcagcttggatgcacactaaatttcccaattagttccattgaaactgtaccagtaagactaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagaa---aaaataaaagcattaacagcaatttgtgaa------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataagaaaaaaggacagt------actaagtggagaaaattagtagatttcagggaacttaataaaagaactcaagacttttgggag---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtgacagtactggatgtgggggatgcatat---ttttcagttcctttagatgaagacttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccagggaaaagatatcaatataatgtgcttccacagggatggaagggatcaccagcaatattccaaagtagcatgacaagaatcttagagccctttagagcaaaaaatccagagatagtcatctatcaatatatggatgacttgtatgtaggatctgacttagaaatagggcaacatagagcaaaagtagaggagttaagagaacatctattaaaatggggacttaccacaccagacaagaaacatcagaaagaacccccatttctttggatgggatatgaactccatcctgataaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacccagggattcaagtaaagcaactttgtaaactccttagggggaccaaagcactaacagacatagtaccattaactgaagaagcagaattagaattagcagaaaacagggaaattttaaaggaaccagtacatggggtatattatgacccatcaaaagacttgatagctgaaatacagaaacaggggtatggccaatggacatatcaaatttaccaagaaccattcaaaaatctgaaaacagggaagtatgcaaaaatg---aggactgcccacactaatgatgtg------aaacagttaacagaggcagtgcaaaaaatagccttggaaagcatagtaatatggggaaag---actcctaaatttagactacccatccaaaaggaaacatgggaaatatggtggacagactattggcaagccacctggattcctgaatgggagtttgttaatacccctcccctagtaaaattatggtaccagctagagaaagaacccatagcagaagtagaaactttctatgtagatggagcagctaatagggaaactaaaataggaaaagcagggtatgttactgatagaggaaggcaaaaa---attgtttctctaactgaaacaacaaatcagaaggctgaattacaagcaattcagttagcattgcaagattcaggatcagaag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+>C.ZA.05.CAP210_5w.GQ999983
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+>C.ZA.05.CAP229_7w.GQ999985
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+>C.ZA.05.CAP239_5w_F1.GQ999991
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+>C.ZA.05.CAP244_8w_F1.GQ999986
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+>C.ZA.05.CAP256_6w.GQ999989
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+>C.ZA.05.CAP63_5w_F4.GQ999976
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+>C.ZA.05.CAP85_5w_F1.GQ999979
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+>C.ZA.05.CAP88_5w_F2.GQ999980
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+>C.ZA.05.CAP8_3w_F2.GQ999972
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+>C.ZA.07.503_07352_C1.KT183196
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+>C.ZA.07.503_10430_2.KT183253
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+>C.ZA.07.705010067_CH067_TF.KC156125
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+>C.ZA.07.705010162_CH162.mo6.KC156115
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+>C.ZA.07.705010198_CH198_TF.KC156130
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+>C.ZA.07.706010164_CH164_TF.KC156127
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+>C.ZA.07.CH107_TF.MN202471
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+>C.ZA.07.CH236_TF.MN202472
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+>C.ZA.08.503_03576_12.KT183128
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+>C.ZA.08.503_06485_10_2.KT183172
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+>C.ZA.08.705010534_CH534.w12.KC156221
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+>C.ZA.08.DEMC08ZA011.JX140666
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+>C.ZA.10.DEMC10ZA001.JX140669
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+>C.ZA.12.DEMC12ZA087.KP109516
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+>C.ZA.12.DEMC12ZA096.KP109517
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-gg--gcgg----cggccggtgagtacgcc-----------------------aattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattacgaggcgaaaaattagataaatgggaaaaaattaggtta---agg------cca---gggggaaagaaacactatatgctaaaacatttagtatgggcaagcagggagctggaaagatttgcacttaaccctggcctgttagaaacatcagaaggctgtaggcaaataataaaacagctacaaccagct---cttcagacaggaacagaggaacttagatcactattcaacacagta---gcaactctctattgtgtacatgaaaagatagaggtacgagacaccaaggaagccttagacaagatagaggaagaacaaaacaaatgtcag------------------------caaaaagaacaacaagcaaaagcg---------------------gctggcgaa------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtacaccaggccctgtcaccgagaactctgaatgcatgggtaaaagtaatagaggagaag------gctttcagcccagaggtaatacccatgtttacagcactatcagaaggagccaccccacaagatttaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaggaggctgcagaatgggataggttacac---ccagtacatgca---gggcctcctgcaccaggccagatg---agagaacctaggggaagtgacatagcaggaactactagtaac---cttcaggaacaaatagcatggatgaca---------ggtaatcca---cct---gtc---ccggta---ggagacatctataaaagatggataattatggggttaaataaaatagtaagaatgtatagccccgtcagcattttggacataagacaaggaccaaaagaaccctttagagactatgtagaccggttcttcaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttgatccaaaatgcgaacccagattgtaagatcattttaaaaggattaggacaaggggctacattagaagagatgatgacagcatgtcagggagtgggaggacctgcccacaaa---gcaagagtgttggctgag------gcaatg---agccaaacaaac------------------------aatggaagcata---atgatg------caaagaaacaat---------ttt---aaaggccctagaaga------attgttaaatgtttcaactgtggcaaggaaggg---cacgtagctagaaactgcagggcccctaggaaaaagggctgttggaaatgtggaaaggagggacaccaaatgaaagactgt---------------aatgagaggcaggctaattttttagggaaaatttggcc---ttcccactc------ggg---gag---gccagggaatttcctccagagcaggccaacagccccaccagcagtagagccaacagc------------------------------------cccaccagc------agagagcttcaagtt------------cgagga---gac---aac---ccccgc------------------------------tccgag---------------aacggaaca------------gagaggcag---------------------------gga---------------atc------acccttaacctccctcaaatcactctttggcaacgaccccttgtctcaataaaagtagggggccagataaaggaagctctcctagatacaggagcagatgatacagtatta---gaagat---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacagtat---gaggaaatacctatagaaatttgtggaaagaaagcaataggtacagtattggtgggacctacacctgtcaac---ataattggaagaaatctgttgactcagcttggatgcacactaaattttccaattagtcccattgatactgtaccagtaaaattaaagccagggatggatggcccaaaagtcaaacaa---tggccattgacagaagag---aaaataaaagcattaacagcaatttgtgaa------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gagaatccatataacactccagtatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagacttttgggaa---gttcaa------tta---ggaata---------------------------ccacatccagcaggattaaaaaagaaa---aaa------tcagtgacagtgctagatgtgggggatgcatat---ttttcagttcctttagatgaagacttcaggaaatatactgcattcaccatacctagtataaacaatgaaacaccagggattagatatcaatacaatgtattaccacagggatggaaaggatcaccagcaatattccagagtagcatgacaaaaatcttagagccctatagagcaaaaaatccagacatagttatctaccaatatatggatgacttgtatgtaggatctgatttagaaataggacaacatagagcaaaaatagaggagttgagagaccatttattgaaatggggatttactacaccagataagaaacatcaaaaagaacccccatttctgtggatgggatatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggccagtcagatttacccagggattaaagtaaggcaactgtgtaaactccttagaggaactaaagcactaacagacatagtaccactgactgatgaagcagaattagaattggcagagaatagggaaatactaaaggaaccagtacatggagtatattatgacccatcaaaggacttgatagctgagctacagaaacaggggcatgatcaatggacatatcaaatttaccaggaaccatttaaaaatctgaagacagggaaatatacaaaaatg---aggactgcccacactaatgatgta------aaacagttaactgaggcagtgcaaaaaatagcccaggaaagcatagtgatatggggaaag---actcctaaatttagactacccatccaaaaggaaacatgggagacatggtggacagactattggcaagccacctggattcctgagtgggagtttgttaatactcctcccctagtaaaattatggtatcaactagaaaaagaacccatagcaggagcagaaaccttctatgtagatggagcaactaatagggaaactaaaatgggaaaagcagggtatgttactgacagaggaagacagaaa---attgtttctctaactgaaacaacaaatcagaaggctgaactacaagcaattcagatagctttacaggactcaggattagaag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+>C.ZA.13.DEMC13ZA152.KU749417
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+>C.ZA.13.HIV1_FR004_D11_CVL_1.MH933705
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+>C.ZA.13.HIV1_FR006_D1_CVL_1.MH933704
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+>C.ZA.14.Pt4.2_S1086.MK643564
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+>C.ZA.14.ZA006EP1C7.MN611462
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+>C.ZA.14.ZA011EP4D1.MN611466
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+>C.ZA.15.Pt1.1_S1052.MK643538
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+>C.ZA.15.ZA015EP3A8.MN611467
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+>C.ZA.16.CAP188_B_W31.MN097551
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+>C.ZA.16.CAP302_B_W11.MN097661
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+>C.ZA.16.CAP316_B_W1.MN097669
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+>C.ZA.16.CAP336_B_W10.MN097680
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+>C.ZA.17.CAP217_B_W1.MN097584
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+>C.ZA.17.CAP287_W13.MN097648
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+>C.ZA.17.CAP288_B_W3.MN097654
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+>C.ZA.89.pZAC_R3714.JN188292
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+>C.ZA.97.97ZA003.AY118165
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+>C.ZA.97.97ZA009.AY118166
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+>C.ZA.97.97ZA012.AF286227
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+>C.ZA.98.98ZA445.AY158533
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+>C.ZA.98.98ZA502.AY158534
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+>C.ZA.98.98ZA528.AY158535
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+>C.ZA.98.CTSC2.AY043176
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+>C.ZA.98.DU151.AY043173
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+>C.ZA.98.TV001.AY162223
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+>C.ZA.98.TV002.AY162224
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+>C.ZA.99.99ZACM9.AF411967
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+>C.ZA.99.99ZALT39.EU293447
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+>C.ZA.99.99ZALT42.EU293448
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+>C.ZA.99.99ZALT45.EU293449
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+>C.ZA.99.99ZALT46.EU293450
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+>C.ZA.99.99ZALT4.EU293444
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+>C.ZA.99.99ZALT5.EU293445
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+>C.ZA.99.99ZATM10.AY228556
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+>C.ZA.99.DU179.AY043174
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+>C.ZA.99.ZASW7.AF411966
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+>C.ZM.02.02ZM108.AB254141
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+>C.ZM.02.02ZM114.AB254146
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+>C.ZM.02.02ZM115.AB254148
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+>C.ZM.02.02ZMBC.AB254149
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+>C.ZM.03.ZM246F_flA10.FJ496186
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+>C.ZM.03.ZM247F_flA1.FJ496195
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+>C.ZM.06.235028_9Mar06_NFLG_TF_Con.MT347678
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+>C.ZM.06.ZM1124F_18May2006_SC_10_N.MT194600
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+>C.ZM.06.ZM1165M_16Mar2006_SC_10_N.MT194738
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+>C.ZM.07.ZM1047M_24Aug2007_SC_1_N.MT194282
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+>C.ZM.07.ZMN133M_16Aug2007_SC_10_N.MT195493
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+>C.ZM.08.305136_23Jul08_NFLG_TF_Con.MT347680
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+>C.ZM.09.DEMC09ZM004.KF716466
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+>C.ZM.09.DEMC09ZM015.KU749426
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+>C.ZM.09.Z331F_15Apr09_PL_NFLG_SGA22.KR820304
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+>C.ZM.09.Z3576M_18Apr09_PL_NFLG_SGA10.KR820326
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+>C.ZM.09.Z3618F_11Jul09_PL_NFLG_SGA11.KR820342
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+>C.ZM.09.Z3678F_23Sep09_PL_NFLG_SGA19.KR820376
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+>C.ZM.09.ZM2006M_13May2009_SC_10_N.MT195145
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+>C.ZM.10.235234_10Mar10_NFLG_TF_Con.MT347679
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+>C.ZM.10.305156_4Jun10_NFLG_TF_Con.MT347681
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+>C.ZM.10.Z4248F_11Jun10_PL_NFLG_SGA1.KR820394
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+>C.ZM.10.Z4248M_4Jun10_PL_NFLG_SGA1.KR820415
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+>C.ZM.10.ZM1788F_04Sep2010_1A_26_N.MT194974
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+>C.ZM.11.DEMC11ZM003.KP109494
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+>C.ZM.11.DEMC11ZM005.KP109495
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+>C.ZM.11.DEMC11ZM006.KF716467
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+>C.ZM.11.DEMC11ZM008.KP109496
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+>C.ZM.11.ZM1658F_01Nov2011_1A_1_N.MT194782
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+>C.ZM.11.ZM634F_18May2011_1A_28_N.MT195378
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tggt-a---------------actagagatc-------cctcagaccaat-ttgg-t-agtgtggaaaaa-tctctagcagtggcg--------cccgaacagggac------------------ccgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct--gaaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----gactggtgagtacgcc----------------------aaattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggcggaaaattagataaatgggaaagaattaggtta---agg------cca---gggggaaagaaacaatataagctaaaacacctagtatgggcaagcagggagctggacagatttgcacttaaccctggccttttagaaacagcagaaggctgtaaacaagcactgcaacagctacaaccagct---cttaagacaggaacagaggaacttaaatcattatacaacacaata---gcaactctctattgtgtacataaaaatatagagataagagacaccaaagaagccttagacagaatagaggaagaacaaaaacaaagtcag------------------------caaaaaacacagcaggcagaagcg---------------------gctggaggg------------------------------aaa------------------------gtcagtcagaattatcctata------------gtacaaaatcttcaagggcagatggtacaccagccgctatcacctagaactttgaatgcatgggtaaaagtaatagaggaaaag------gctttcagcccagaggtaatacccatgtttacagcattgtcagaaggagccaccccacaagatctaaacaccatgttaaatacagtggggggacatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaggaagctgcagaatgggataggttacat---ccagtgcccgca---gggcctgttgcaccaggccagata---agagaccccagaggaagtgacatagcgggaactactagtacc---cttcaggaacaaataacatggatgaca---------agtaaccca---cct---atc---ccagtg---ggagacatctataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagcattttggacataagacaaggaccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaacccagactgtaagaccattttaagagcattgggaccaggggcttcattagaagaaatgatgacagcatgtcagggagtgggaggaccaggccacaaa---gcaagggttttggctgag------gcaatg---agccaagcaaac------------------------aatgcaaatata---atgatg------cagagaaacaat---------ttc---aagggctctaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---catatagccagaaattgcagggcccctaggaagaaaggctgttggaaatgtggaaaggaaggacatcaaatgaaagactgc---------------actgagaggcaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---aag---gccagggaatttcctccagagcaggccagagccaacagc------------------------------------cccaccagagccaacagctccaccagc------agagagcttcagatt------------caagga---gac---agc---acccac------------------------------tccgca---------------gcaggagtc------------gaaagacag---------------------------gga------------------------acccttaatttccctcaaatcactctttggcagcgaccccttgtctcaataaaaatagggggccagataaaagaggctctcttagatacaggagcagatgatacagtatta---gaagaa---atgaatttgccaggaaaatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtat---gatcaaatacctatagaaatttgtggaaaaaaggctataggtgcagtgttagtaggacctacacctgtcaac---ataattggaagaaacatgttgactcagcttggatgtacactaaattttccaattagtcctattgagactgtaccagtaaaattaaagccagggatggatgggccaaaggttaaacaa---tggccattatcagaagaa---aaaataaaagcattaacagcaatctgtgag------gaaatggaaaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccagtatttgccataaaaaagaaggacagt------actaagtggagaaaattagtagatttcagggagcttaataaaagaactcaagatttttgggaa---gttcaa------cta---ggaata---------------------------ccacacccagcaggattgaaaaagaaa---aaa------tcagtgacagtactggatgtgggggatgcatat---ttttcagttcctttagatgaaaacttcaggaaatatactgcatttaccatacccagtataaataatgaaacaccagggattagatattgttataatgtgcttccacagggatggaaaggatcaccagcaatatttcaaagtagcatgacaaaaatcctagcgccctttagagcacaaaatccagaaatagttatctatcaatatatggatgacttatatgtaggatctgatttagaaatagggcaacatagagcaaaaatagaagagttaagagaacacttattaaaatggggatttactacaccagacaagaaacatcagaaagagcccccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggag---agctggactgtcaatgatatacagaaaatagtgggaaaattgaactgggcaagtcagatttactcagggattaaagtaaagcaactgtgtagactccttaggggagccaaagcactaacagatgtagtaccactaactaaagaagcagaattagagttggcagaaaacagggaaattctaaaagaaccagtacatggagtatattatgacccatcaaaagatttaatagctgaaatacagaaacagggccatgaccaatggacatatcaaatttaccaagaaccattcaaaaacctgaaaacaggaaagtatgcaagaatg---aggactgcccacactaatgatgta------agacagttaacagaggcagtgcaaaaaatagccctggaaagcatagtaatatggggaaag---actcctaaatttagactacccatacaaaaagaaacatgggagacatggtggacagaatattggcaagccacctggattcctgagtgggagtttgttaatacccctcccttggtaaagttgtggtaccagctggagaaagaacccataatgggagcagaaacattctatgtggatggagcagctaatagggaaactaaactaggaaaagcagggtatgttactgatagaggaaggcagaaa---gttatttctataactgatacaacaaatcagaagactgaattacaagcaatacagctggctttacaagattcagggtcagaag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+>C.ZM.12.ZM1123M_10Jan2012_1A_1_N.MT194468
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+>C.ZM.89.ZAM18.AB485645
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+>C.ZM.96.96ZM651.AF286224
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+>C.ZM.x.HIV1084i.AY805330
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tcttgggagcagca---ggaagcactatgggcgcggcgtca---ctaacgctgacggtacaggcc---aga------caa---ttattg---tctggtatagtgcaacagcaa---aacaatttg---ctgagggctatagaggcgcaacagcatatgttgcaactcacggtctggggcattaagcagctccag---gcaagagtcttggctatagaaagatacctacaggatcaacagctcctaggaatttggggctgctctggaaaactcatctgcaccactgatgtgccttggaactct---agt---tgg------------------------------------agtagtaaatcttatgaggacatttgg---------aca---aatatgacctggatgcag---tgg---gat-aaagaaattaataattacacaaacacaatatatcagttgcttgtagactcgcaa-acccagcaggaa-aaaaatgaaagggagttactagcattggacagttggaaaaatctgtggaattggtttaacataacaaattggctatggtatata-aaaatattcataatgatagtaggaggcttgataggttta-agaataatttttgctgtgctctctatggtaaatagagttaggcagggatactcacctctgtca---tttcag---acccttaccccaaac------ccgagggga------cccgacagg------ctcggaagaatcgaagaagaaggtggagagcaagacagagacagatccattcgattagtgagcggattcttagcgcttgcctgggacgacctgcggagcctgtgccttttcagctac---caccgattgagagactgcatattgattgtagcgagggcagcggaa---ctt---ctg---ggacgcagcagtctcaggggactacag------------------------aaggggtgg------gaagcccttaag---tatctg---------ggaagccttgtgcagtattggggtctagagctaaaaaagagtgct--attagtctgcttgataccacagcaatagcagtagctgaa-ggaacagatagaattataaaattaatacaaagaatttgtaga------gctatctgcaacatacctaga---agaataagacagggctttgaagcagct------ttg-------caa---taa--------------------------------------aatggggggcaagtggtcaaaa------agcagtata---gtt---ggatggcctgctgtaagagaaagaataagacaaact------------------------------------------------------------gctccagca------------------------------gcaacaggagtaggagca---gcgtctcaagacttagatacacatggggcacttacaaccagcaacacagttagcaacaatgctgat---tgtgcctggttggaagca---------caagaggag---------aaa---gacgaggtaggctttccagtcagacctcaggtacctttaagaccaatgacttataaggcagcattc------gatctcagcttctttttaaaagaaaaggggggactg---gatgggttaatttactccaagaaaaggcaagacatc---------cttgatctgtggatctatcacaca-caa---ggcttcttccctgattggcaa---aactacacaccgggaccaggggtcagatatccactgacctttggatggtgcttcaagctagtgccagttgacccaagggaagtagaagaa------gccactgaagga------gagaacagctgtttactacaccctatgagcctgcatggactggaagatgcg---gacaga---gaagtattaaggtggaagtttgacagtcacctagcg-cacagacacatggcccgcgagctacat---ccggagttt------------------------tacaaagactgctgac--------------------------------------------acagaa------------------------------------------------------------------------gggactttcc----------------gct----------------------------------------gggactttccactgg---------------------------------------------------------------------ggcgttccaggaggt------------gtggtc-tgggcgggact-----------gggg-agtg-gc-cagccc--tcag-a-----tgctgcat--ataagcag-c-tgcttttc-gc-t-tg-ta--ctgg-g----tc-tctc-ta--------g-gtag----a--ccagat---------------------------------------------------------------------ctgag---------------cc-cggg-agctc--------tctgg-----------c------tatc-t-agggaac-ccactgctt--aa-gcct----c-aat--aaagc-ttgc---c-----------tt--ga--g-tgct-ctaag-tagtgtgtgcccgtctg-t--tgt-------------gt-gact-c--------------tggt-aact-agaga-tccctcagac-cc-----------------------------------------------------------------------------------------------------------------------
+>C.x.03.LA07SeJe.KU168262
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+>D.BR.10.10BR_RJ095.KJ787684
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+>D.CD.02.CG_0382_02V_NGSID3.KY392769
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+>D.CD.02.LA18ZiAn.KU168272
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+>D.CD.03.LA17MuBo.KU168271
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+>D.CD.83.ELI.K03454
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+>D.CD.83.NDK.M27323
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+>D.CD.87.PBS5635.MH705152
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+>D.CM.10.DEMD10CM009.JX140670
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+>D.KE.97.ML415_2.AY322189
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+>D.SN.90.SE365.AB485648
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+>D.TD.99.MN011.AJ488926
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+>D.UG.05.p190049.JX236668
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+>D.UG.07.p191647.JX236670
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+>D.UG.07.p191882.JX236673
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+>D.UG.08.p191859.JX236672
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+>D.US.07.HIV_US_BID_V3121_2007.JQ403079
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+>D.ZA.84.R2.AY773338
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+>D.ZA.85.R286.AY773340
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+>D.ZA.90.R1.EF633445
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+>F1.BE.93.VI850.AF077336
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+>F1.BG.08.S_08_002.MH746263
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+>F1.BR.01.01BRRJSB153.MG365763
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+>F1.BR.02.02BR082.FJ771006
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+>F1.BR.06.06BR564.FJ771008
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+>F1.BR.06.06BR579.FJ771009
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+>F1.BR.07.07BR844.FJ771010
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+>F1.BR.10.10BR_PE107.KJ849782
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+>F1.BR.10.10BR_RJ055.KT427774
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+>F1.BR.10.DEMF110BR015.KU749395
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+>F1.BR.11.11BRRJPR90.MG365768
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+>F1.BR.12.12BRRJPR51.MG365764
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+>F1.BR.93.93BR020_1.AF005494
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+>F1.ES.02.ES_X845_4.FJ670516
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+>F1.FR.04.LA22LeRe.KU168276
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+>F1.FR.96.96FR_MP411.AJ249238
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+>F1.RO.03.LA20DuCl.KU168274
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+>F1.x.03.LA21LeAn.KU168275
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+>F2.CM.01.A1699.MH705144
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+>F2.CM.11.DEMF211CM025.KU749420
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+>G.BG.09.V_09_011.MH746255
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+>G.CD.03.LA23LiEd.KU168277
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+>G.CD.87.P406.MH705155
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+>G.CD.87.PBS1191.MH705134
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+>G.CM.05.05CMBDSH19.MN153484
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+>G.CM.05.144_26.MH705145
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+>G.CM.06.740_14.KP718915
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+>G.CM.07.920_49.KP718923
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+>G.CM.08.789_10.KP718925
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+>G.CM.10.DEMG10CM008.JX140676
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+>G.CN.13.GZ8H3748.13.MH431770
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+>G.NG.11.DEMG11NG008.KY953202
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+>G.PT.x.PT2695.AY612637
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+>G.PT.x.PT3037.FR846408
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+>G.x.03.LA24HoCe.KU168278
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+>H.CD.01.CG_0536_02_NGSID14.KY392777
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+>H.CD.01.CG_0538_02_NGSID15.KY392778
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+>H.CD.04.LA19KoSa.KU168273
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+>H.CF.02.LA25LeMi.KU168279
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+>H.CF.90.056.AF005496
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+>J.AO.93.93AOHDC253.KU310620
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+>J.CD.02.CG_0331_02V_NGSID13.KY392776
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+>K.CD.97.97ZR_EQTB11.AJ249235
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+>K.CM.96.96CM_MP535.AJ249239
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+>L.CD.83.83CD003_Z3.AF286236
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+>01_AE.CM.03.U7957.MN116207
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+>01_AE.CM.03.U8216.MN116208
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+>01_AE.CM.11.1156_26.KP718930
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+>01_AE.CN.02.YN0221.JX112861
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+>01_AE.CN.02.YN0229.JX112863
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+>01_AE.CN.05.05GX001.GU564221
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+>01_AE.CN.05.05GX002.GU564222
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+>01_AE.CN.05.05GX013.GU564224
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+>01_AE.CN.05.05GX034.GQ845124
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+>01_AE.CN.05.05GX079.GQ845125
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+>01_AE.CN.05.05GX128.GQ845126
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+>01_AE.CN.05.05GX142.GU564227
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+>01_AE.CN.05.05GX162.GU564229
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+>01_AE.CN.05.FJ051.DQ859178
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+>01_AE.CN.05.FJ053.DQ859179
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+>01_AE.CN.05.Fj056.EF036529
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+>01_AE.CN.05.Fj065.EF036534
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+>01_AE.CN.06.06GX239.GU564230
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+>01_AE.CN.06.Fj064.EF036533
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+>01_AE.CN.07.07CNYN312.KF835499
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+>01_AE.CN.07.07CNYN315.KF835502
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+>01_AE.CN.07.07CNYN316.KF835503
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+>01_AE.CN.07.07CNYN317.KF835504
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+>01_AE.CN.07.07CNYN318.KF835505
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+>01_AE.CN.07.07CNYN326.KF835513
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+>01_AE.CN.07.07CNYN327.KF835514
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+>01_AE.CN.07.07CNYN329.KF835516
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+>01_AE.CN.07.07CNYN332.KF835518
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+>01_AE.CN.07.07CNYN333.KF835519
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+>01_AE.CN.07.07CNYN337.KF835523
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+>01_AE.CN.07.07CNYN342.KF835527
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+>01_AE.CN.07.07CNYN343.KF835528
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+>01_AE.CN.07.07CNYN354.KF835533
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+>01_AE.CN.07.07CNYN357.KF835536
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+>01_AE.CN.07.07CNYN359.KF835538
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+>01_AE.CN.07.07CNYN364.KF835542
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+>01_AE.CN.07.07CNYN366.KF835543
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+>01_AE.CN.07.FJ070013.JX112810
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+>01_AE.CN.07.FJ070017.JX112811
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+>01_AE.CN.07.FJ070035.JX112814
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+>01_AE.CN.07.FJ070040.JX112817
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+>01_AE.CN.07.GD070058.JX112820
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+>01_AE.CN.07.GD070059.JX112821
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+>01_AE.CN.07.GD070090.JX112823
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+>01_AE.CN.07.GD070120.JX112827
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+>01_AE.CN.07.GX070003.JX112829
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+>01_AE.CN.07.GX070005.JX112830
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+>01_AE.CN.07.GX070006.JX112831
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+>01_AE.CN.07.GX070076.JX112834
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+>01_AE.CN.07.GX070143.JX112835
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+>01_AE.CN.07.GX070145.JX112836
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+>01_AE.CN.07.GX070154.JX112838
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+>01_AE.CN.07.GZ070127.JX112845
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+>01_AE.CN.07.JS070901.JX112850
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+>01_AE.CN.07.JS071101.JX112853
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+>01_AE.CN.07.LN070008.JX112854
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+>01_AE.CN.07.LN070013.JX112856
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+>01_AE.CN.09.1119.HQ215553
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+>01_AE.CN.09.YN09P0011.JX112867
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+>01_AE.CN.09.ZK056.JX112870
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+>01_AE.CN.10.CYM105.JX112798
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+>01_AE.CN.10.CYM124.JX112799
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+>01_AE.CN.10.CYM136.JX112800
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+>01_AE.CN.10.CYM138.JX112801
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+>01_AE.CN.10.CYM139.JX112802
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+>01_AE.CN.10.CYM140.JX112803
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+>01_AE.CN.10.CYM143.JX112804
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+>01_AE.CN.10.DE00110CN007.KP109506
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+>01_AE.CN.10.DE00110CN009.KP109507
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+>01_AE.CN.10.JL100005.JX112846
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+>01_AE.CN.10.JL100020.JX112849
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+>01_AE.CN.10.YNFL03.KC870029
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+>01_AE.CN.12.DE00112CN011.KP109508
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+>01_AE.LA.11.VI38M3815.MG760415
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+>01_AE.LA.11.VI50M3793.MG760425
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+>01_AE.MM.99.mCSW105.AB097872
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+>01_AE.PH.15.DE00115PH012.KY658688
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+>01_AE.PH.16.DE00116PH013.MH078562
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+>01_AE.TH.01.LA09DuCe.KU168264
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+>01_AE.TH.03.TH7229.KU168309
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+>01_AE.TH.04.04TH613543.JN248330
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+>01_AE.TH.04.AA075a_WG7.JX447542
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+>01_AE.TH.04.BKM.DQ314732
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+>01_AE.TH.05.05TH130087.JN248339
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+>01_AE.TH.05.05TH327568.JN248341
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+>01_AE.TH.05.AA064a_WG2.JX447413
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+>01_AE.TH.05.AA107a_wg4.JX448022
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+>01_AE.TH.07.AA072a03.JX447503
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+>01_AE.TH.08.AA108a_WG6.JX448028
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+>01_AE.TH.08.MERLBDTRC9.JN860768
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+>01_AE.TH.11.2543513P000FL_Sj.MG989495
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+>01_AE.TH.11.2545349P000FL_Sa.MG989516
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+>01_AE.TH.11.2546340P000FL_Sg.MG989527
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+>01_AE.TH.11.2549114P000FL_Sa.MG989561
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+>01_AE.TH.11.40512v02_03.MK116905
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+>01_AE.TH.12.2544477P000FL_Sa.MG989509
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+>01_AE.TH.12.2545864P000FL_Sa.MG989523
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+>01_AE.VN.14.DE00114VN001.MT222954
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+>01_AE.VN.97.97VNAG204.FJ185247
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+>01_AE.VN.97.97VNAG206.FJ185248
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+>01_AE.VN.97.97VNAG210.FJ185251
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+>01_AE.VN.97.97VNAG212.FJ185252
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+>01_AE.VN.97.97VNAG218.FJ185255
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+>01_AE.VN.97.97VNHCM314.FJ185241
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+>01_AE.VN.97.97VNHCM319.FJ185242
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+>01_AE.VN.98.98VNND15.FJ185235
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+>02_AG.CI.16.DE00216CI019.MH078536
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+>02_AG.CI.16.DEURF16CI022.MH078539
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+>02_AG.CM.00.LA10GuVa.KU168265
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+>02_AG.CM.03.CM1193_8.KU168304
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+>02_AG.CM.04.459_16.MH705136
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+>02_AG.CM.07.CM100_17.KU168310
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+>02_AG.CM.08.08CMBDSH9.MN153494
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+>02_AG.CM.08.DE00208CM001.JX140646
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+>02_AG.CM.08.DE00208CM004.JX140647
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+>02_AG.CM.10.DE00210CM013.KF859739
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+>02_AG.CM.10.DE00210CM019.KU749419
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+>02_AG.CM.15.DE00215CM060.MT222937
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+>02_AG.DE.09.701114.KT124792
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+>02_AG.FR.91.DJ263.AF063223
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+>02_AG.GH.03.03GH181AG.AB286855
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+>02_AG.GH.03.GHNJ188.AB231896
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+>02_AG.GH.03.GHNJ196.AB231898
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+>02_AG.GH.97.97GH_AG1.AB049811
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+>02_AG.GH.x.I_2496.AB485633
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+>02_AG.GW.14.DE00214GW002.MH078541
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+>02_AG.GW.14.DE00214GW005.MH078542
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+>02_AG.GW.14.DE00214GW009.MH078544
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+>02_AG.GW.14.DEURF14GW040.MN703132
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+>02_AG.KR.12.12MHI11_10746.KF561437
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+>02_AG.KR.12.12MHR9.KF561435
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+>02_AG.LR.x.POC44951.AB485636
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+>02_AG.NG.11.11NG050356.KX389643
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+>02_AG.NG.11.DE00211NG010.KY953198
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+>02_AG.NG.12.12NG060304.KX389647
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+>02_AG.SE.11.SE602024.KP411845
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+>02_AG.SE.94.SE7812.AF107770
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+>02_AG.UG.10.DEURF10UG006.KF716488
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+>02_AG.US.06.502_2696_FL01.JF320297
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+>02_AG.x.00.LA11ZaCh.KU168266
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+>02_AG.x.00.LA12FroG.KU168267
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+>05_DF.BE.x.VI1310.AF193253
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+>05_DF.ES.99.X492.AY227107
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+>06_cpx.AU.96.BFP90.AF064699
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+>06_cpx.BF.x.LA14AAS287.KU168269
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+>06_cpx.CD.x.BCF_Dioum.AB485660
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+>06_cpx.GH.03.03GH173_06.AB286851
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+>06_cpx.ML.95.95ML127.AJ288982
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+>06_cpx.ML.95.95ML84.AJ245481
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+>07_BC.CN.05.XJDC6431_2.EF368372
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+>07_BC.CN.05.XJDC6441.EF368370
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+>07_BC.CN.05.pXJDC6291_13.KC492737
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+>07_BC.CN.07.07CNYN303.KF835494
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+>07_BC.CN.07.07CNYN323.KF835510
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+>07_BC.CN.07.07CNYN324.KF835511
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+>07_BC.CN.07.07CNYN349.KF835532
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+>07_BC.CN.98.98CN009.AF286230
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+>07_BC.TW.13.pCRF07.KF234628
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+>08_BC.CN.07.07CNYN302.KF835493
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+>08_BC.CN.07.07CNYN306.KF835495
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+>08_BC.CN.07.07CNYN307.KF835496
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+>08_BC.CN.07.07CNYN310.KF835497
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+>08_BC.CN.07.07CNYN313.KF835500
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+>08_BC.CN.07.07CNYN320.KF835507
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+>08_BC.CN.07.07CNYN322.KF835509
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+>08_BC.CN.07.07CNYN344.KF835529
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+>08_BC.CN.07.07CNYN346.KF835530
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+>08_BC.CN.07.07CNYN350.KF835531
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+>08_BC.CN.07.07CNYN351.KF835535
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+>08_BC.CN.07.07CNYN355.KF835534
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+>08_BC.CN.07.07CNYN363.KF835541
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+>08_BC.CN.07.07CNYN369.KF835545
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+>08_BC.CN.07.07CNYN371.KF835547
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+>09_cpx.CI.00.00IC_10092.AJ866553
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+>09_cpx.SN.95.95SN1795.AY093603
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+>09_cpx.SN.95.95SN7808.AY093604
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+>10_CD.TZ.96.96TZ_BF061.AF289548
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+>10_CD.TZ.96.96TZ_BF071.AF289549
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+>10_CD.TZ.96.96TZ_BF110.AF289550
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+>11_cpx.CM.02.A1575.KP718934
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+>11_cpx.CM.02.A1774.KP718935
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+>11_cpx.CM.04.119_28.KP718937
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+>11_cpx.CM.04.1230_24.KP718938
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+>11_cpx.CM.04.260_50.KP718936
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+>11_cpx.CM.06.263_26.KP718914
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+>11_cpx.CM.08.1252_11.KP718929
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+>11_cpx.CM.11.DEURF11CM015.KP109503
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+>11_cpx.CM.97.MP818.AJ291718
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+>11_cpx.FR.99.MP1298.AJ291719
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+>11_cpx.FR.99.MP1307.AJ291720
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+>11_cpx.x.03.LA15PoCa.KU168270
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+>12_BF.CN.18.10_097.MT712270
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+>12_BF.UY.99.URTR23.AF385934
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+>13_cpx.CM.08.228_10.KP718924
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+>13_cpx.CM.08.833_62.KP718926
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+>13_cpx.CM.96.96CM_1849.AF460972
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+>13_cpx.CM.96.96CM_4164.AF460974
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+>15_01B.TH.05.05TH637314.JN248352
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+>18_cpx.CM.11.B4043_15.KP718931
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+>20_BG.US.18.5108_wk_2_3_I20.MW062981
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+>22_01A1.CM.10.LB011.JN864051
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+>22_01A1.CM.10.LB013.JN864058
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+>23_BG.CU.03.CB347.AY900572
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+>24_BG.CU.03.CB471.AY900575
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+>26_A5U.CD.02.02CD_KS069.FM877780
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+>26_A5U.CD.97.97CD_KTB119.FM877777
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+>27_cpx.CD.03.CG_0077_01.MN116204
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+>27_cpx.CD.97.97CDKTB49.AJ404325
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+>28_BF1.BR.05.0614SV.JF804809
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+>28_BF1.BR.05.0679SV.JF804812
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+>28_BF1.BR.99.BREPM12313.DQ085872
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+>28_BF1.BR.99.BREPM12609.DQ085873
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+>28_BF1.BR.99.BREPM12817.DQ085874
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+>29_BF1.BR.01.BREPM16704.DQ085876
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+>29_BF1.BR.05.0063SP.JF804806
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+>29_BF1.BR.99.BREPM11948.DQ085871
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+>31_BC.BR.04.04BR137.AY727526
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+>31_BC.BR.04.04BR142.AY727527
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+>32_06A6.EE.06.A14.KM606632
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+>33_01B.MY.05.05MYKL015_2.DQ366660
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+>35_A1D.AF.06.007H.GQ477450
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+>37_cpx.CM.06.1130_39.KP718917
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+>39_BF1.BR.03.03BRRJ327.EU735536
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+>39_BF1.BR.04.04BRRJ179.EU735535
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+>40_BF1.BR.04.04BRRJ115.EU735538
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+>40_BF1.BR.05.05BRRJ055.EU735537
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+>40_BF1.BR.05.05BRRJ200.EU735539
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+>46_BF1.BR.01.01BR087.DQ358801
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+>46_BF1.BR.01.01BR125.DQ358802
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+>46_BF1.BR.01.01BRRJUD508.MG365771
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+>46_BF1.BR.07.07BR_FPS625.HM026456
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+>46_BF1.BR.07.07BR_FPS742.HM026457
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+>46_BF1.BR.07.07BR_FPS783.HM026458
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+>46_BF1.BR.07.07BR_FPS810.HM026459
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+>46_BF1.BR.07.07BR_FPS812.HM026460
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+>47_BF1.ES.08.X2457_2.FJ670529
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+>48_01B.MY.07.07MYKT016.GQ175882
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+>48_01B.MY.07.07MYKT021.GQ175883
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+>55_01B.CN.10.HNCS102056.JX574661
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+>55_01B.CN.15.BL1947_00.MW110767
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+>57_BC.CN.07.341.HM776939
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+>57_BC.CN.09.09YNLX19sg.KC899008
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+>57_BC.CN.09.1439.JX679207
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+>59_01B.CN.07.GD070126.KF011494
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+>59_01B.CN.11.11CN.LNSY300876.KJ484434
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+>59_01B.CN.12.12CN.YNKM200199.KJ484435
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+>61_BC.CN.10.JL100010.KC990124
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+>64_BC.CN.09.09YNLX047sg.KC898994
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+>64_BC.CN.09.09YNLX219037sg.KC899009
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+>65_cpx.CN.10.YNFL02.KC870028
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+>70_BF1.BR.10.DE07010BR033.KU749388
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+>71_BF1.BR.10.10BR_PE008.KJ849759
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+>71_BF1.BR.10.10BR_SP026.KT427816
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+>72_BF1.BR.03.BREPM1029.EF637052
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+>72_BF1.BR.10.10BR_MG002.KJ671534
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+>76_01B.JP.12.N628.MN187303
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+>85_BC.CN.14.14CN_SCYB12.KU992936
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+>85_BC.CN.14.14CN_SCYB18.KU992937
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+>85_BC.CN.14.14CN_SCYB1.KU992928
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+>85_BC.CN.14.14CN_SCYB20.KU992930
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+>85_BC.CN.14.14CN_SCYB2.KU992929
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+>85_BC.CN.14.14CN_SCYB3.KU992931
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gcg--------cccgaacagggac------------------gcgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc-----------------------aattatatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagaggggaaaaattagataaatgggaaaaaattaggtta---agg------cca---gggggaaagaaacactatatgctaaaacacgtagtatgggcaagcagggagctggacagatttgcacttaaccctggccttttagagacatcagagggctgtaaacaaataatgaaccagttacaaccagct---cttaagacagcaacagaagaacttagatcattattcaacacagta---gcaactctctattgtgtacataaagggatagatgtacgagacaccaaagaagccttagacaagatagaagaagaacaaaaccaaattcag------------------------caaaaaacacagcaggaaaaagag---------------------gctgacggg------------------------------aag------------------------gtcagtcaaaattatcctata------------gtgcagaatattcaagggcaaatggtacatcaggccatatcaccaagaactttaaatgcatgggtaaaagtggtagaagagaag------gcttttagcccagaggtaatacccatgttttcagcactatcagaaggagccaccccacaagatttaaacaccatgctaaatacagtggggggacatcaa---gcagccatgcaaata---ttaaaagat---acaatcaatgaagaggctgcagagtgggatagactgcat---ccagtacatgca---gggccagtagcaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaactactagtact---cttcaggagcaaatagcatggatgacg---------agtaatcca---cct---gtt---ccagta---ggagacatttataaaagatggataattctgggattgaataaaatagtaagaatgtatagccctaccagcattctggacataaaacaagggccaaaggaaccctttagagactatgtagatcggttctttaaaactttaagagctgaacaagctacacaagatgtaaaaaattggatgacagacaccttgttagtccaaaatgcgaacccagattgtaaaaccattttaagagccttaggaccaggggcttcaatagaagaaatgatgacagcatgtcagggagtgggaggacctagccataaa---gcaagagtgttggctgag------gcaatg---agccaaacaaac---------------------------aatgccata---atgatg------cagagaagcaat---------ttt---aaaggtgccaaaaga------attgttaaatgtttcaactgtggcaaggaaggg---catatagctagaaactgcagggcccctaggaaaaagggctgttggaaatgtggaaaagaaggacaccaaatgaaagactgt---------------actgaaaggcaggcgaattttttagggaaattttggcc---ttcccacaa------ggg---gag---gccagggaatttcatccagagcagaccagagccaacagc------------------------------------------------------cccaccagc---------------------------------agagga---ggc---aac---cccagc------------------------------tccgaa---------------ggaggaaca------------gaaagacag---------------------------gga------------------------agccttaatttccctcagatcactctttggcagcgaccccttgtctcaataaaagtagggggccagataaaagaggctctcttagacacaggagcagatgatacagtattg---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacaatat---gagcaaataactattgaaatttgtggaaaaagggctataggtacagtattagtgggacctacacctgtcaac---ataattggaagaaacctgttgactcagcttggttgcactttaaattttccaatcagtcccattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaggtaaaacaa---tggccattgacagaagag---aaaataaaagcattaacagagatttgtgat------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gaaaatccatataacactccaatatttgccataaaaaagaaggacagt------actaagtggagaaagttagtagatttcagggaactcaataaaagaactcaagatttttgggaa---gttcaa------tta---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtgacggtactggatgtgggggatgcttat---ttttcagttcctttagatgaagacttcaggaaatatactgcattcaccatacctagtgtaaacaatgaaacaccagggattaggtatcaatacaatgtacttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatcttagaaccttttagaaaacagaatccagacatagttatctatcaatacatggatgacttgtatgtaggatctgacttagaaatagggcagcatagaacaaaaatagaagcactgagaggacatctgttaaagtggggattcaccacaccagacaagaaacatcagaaagaaccaccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctgccagaa---aaggat---agctggactgtcaatgatatacagaagttagtgggaaaattaaactgggcaagtcagatttacccaggaattaaagtaaagcaactttgtaaactccttaggggggccaagaaactaacagacatagtaccgctaactgaagaagcagaattagaattggcagaaaacagggaaattctaaaagaaacagtacatggagtatattatgacccattaaaagacttgatagctgaaatacagaaacaagggcaggatcaatggacatatcaaatttaccaagaaccattcaaaaatctaaaaacaggaaagtatgcaaaaaag---aggactgcccacactaatgatgta------agacaattaaccgaggctgtgcagaaaatagccatggaaagcatagtaatatggggaaag---actcctaaatttagattacccatccagaaagaaacatgggaggcatggtggacagactattggcaagccacttggatccctgagtgggaatttgttaatacccctcccttagtaaaattatggtaccaactggagaaagatcccatagcaggagcagaaactttctatgtagatggagcagctaatagggagactaaaataggaaaagcagggtatgttactgacagaggaaggaagaaa---gttgtctctctaactgaaacaacaaatcagaagactgaattgcaagcaatttatatggctttgcaagattcaggatcagaag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+>85_BC.CN.14.14CN_SCYB4.KU992932
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+>85_BC.CN.14.14CN_SCYB7.KU992934
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+>85_BC.CN.14.14YNBS57II.MK258683
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+>87_cpx.CN.09.09YNLC497sg.KC898992
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+>87_cpx.CN.09.09YNRL215050sg.KC899012
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+>88_BC.CN.05.05YNRL25sg.KC898979
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+>89_BF1.PE.13.DEURF13PE006.MH078556
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+>92_C2U.CD.02.CG_0151_02V_NGSID1.KY392767
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+>92_C2U.x.04.LA08SySa.KU168263
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+>96_cpx.CN.10.JL.RF01.KF850149
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+>96_cpx.CN.13.13YNBS54IDU.MG518476
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+>96_cpx.CN.13.13YNBS66IDU.MG518477
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+>97_01B.LA.12.BL50F5250.MG760379
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+>98_06B.FR.09.A_Bordeaux.MH479275
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+>100_01C.CN.13.YNLC28.MH909569
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+>100_01C.CN.13.YNLC30.MH909570
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+>101_01B.CN.07.07CNYN370.KF835546
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+>109_0107.CN.14.LS11584.MT919517
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+>110_BC.CN.07.07CNYN338.KF835524
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+>112_01B.CN.18.18110456.MW018130
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+>113_0107.CN.17.BL3128_00.MW018132
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+>113_0107.CN.19.BL3957_00.MW018135
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+>115_01C.CN.13.kang019a_NFL.KJ778895
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+>0102.CM.05.260_27.MN116210
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+>0102A.CM.07.567_16.KP718921
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+>0102A.CM.07.663_13.KP718922
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+>0102A1.CM.06.890_05.MN116211
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+>0107.CN.07.JL070032.KC990127
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+>0107.CN.07.MSM0720.KC833436
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+>0107.CN.10.10LNA015.KU051564
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+>0107.CN.10.JL.RF03.KJ184176
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+>0107.CN.11.JL.RF09.KJ184180
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+>0107.CN.12.kang124_NFL.KJ778897
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+>0107.CN.13.BJMP3002.KM974719
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+>0107.CN.14.BJ2015EU16.MH029899
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+>0107.CN.15.LN321945.KX434796
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+>0107.CN.15.SN121.MF373389
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+>0107.CN.15.YA1996_00_NFLG.MF084205
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+>0107.CN.16.GX2016EU10.MH377336
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+>0107.CN.17.TJ20170316.MH220193
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+>0107.CN.17.TJIH0345.MH801989
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+>0107.CN.18.18GZ028.MK474158
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+>0107.CN.18.THIH0172.MK650464
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+>0107.CN.19.2019QZLSIDU253.MN643057
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+>0108.CN.12.GXDY_1299_NLFG.KF541292
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+>01A1F2.CM.07.BS72.KR017779
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+>01B.CN.10.JL.RF07.KF859773
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+>01B.JP.13.D9451.MN187301
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+>01B.MM.99.mCSW104.AB097867
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+>01B.MY.05.05MYKL043_1.DQ366666
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+>01B.PH.16.DEURF16PH011.MH078564
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+>01B.TH.04.04TH321566.JN248322
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+>01BC.CN.07.07CNYN330.KF835517
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+>01BC.CN.07.07CNYN334.KF835520
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+>01BC.CN.07.07CNYN358.KF835537
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+>01BC.CN.10.DH02.KF250395
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+>01BC.CN.10.JL.RF05.KJ184177
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+>01BC.CN.13.S15_5h4_3h2_FL.KP170487
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+>01BC.CN.15.zj032.KX159285
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+>01BC.CN.16.GX2016EU23.MG064457
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+>01BC.CN.16.JL16013.MH051842
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+>01C.CN.18.GZ18021_10.MK371104
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+>01F1G.CD.01.CG_0070_01.MN116203
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+>01F1G.CD.02.CG_0427a_02V.MN116206
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+>01F2.CM.17.17CMMDC6542.MN153476
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+>01F2G.CM.02.LT31.JN864056
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+>0206.BF.x.LA13BF17.KU168268
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+>0206.BJ.13.LA58Benin.KU168301
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+>0206.GH.03.03GH195AG_06.AB286853
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+>0209.CI.01.01IC_PCI118.AJ866556
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+>0209.CI.16.DEURF16CI004.MH078537
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+>0209.GH.97.G829.AF184155
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+>0222.CM.06.NYU488.JN864047
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+>0222.CM.10.LB045.JN864053
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+>02A.CI.16.DEURF16CI011.MH078538
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+>02A.CM.08.DEURF08CM005.KF716465
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+>02A.GW.14.DEURF14GW011.MH078547
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+>02A.GW.14.DEURF14GW016.MH078549
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+>02A.GW.14.DEURF14GW019.MH078550
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+>02A.SI.15.Sample54_SI503.MN736705
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+>02A1.EE.06.A48.KM606636
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+>02A1.GH.97.97GH_AG2.AB052867
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+>02A1.GW.06.DL4186.KR067668
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+>02A1.PK.15.PK025.KX232617
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+>02A1.PK.15.PK038.KX232627
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+>02A1F2.CM.10.DEURF10CM024.KU749421
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+>02A3.CM.07.BS13.KR017772
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+>02A3.GH.03.GHNJ176.AB231894
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+>02D.GH.03.GHNJ193.AB231897
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+>02D.GH.03.p03GH194AG09.AB480044
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+>02F2.CM.11.NYU6541_6_bulk.MK086126
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+>02F2G.CM.02.LT66.JN864057
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+>02G.GH.03.p03GH179AG_G02.AB480047
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+>02G.NG.11.DEURF11NG013.MT222940
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+>02GK.CI.01.01IC_PCI123.AJ866557
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+>02O.CM.97.97CA_MP645M_O.AJ239083
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+>06A1.BJ.x.B76.AJ293865
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+>06G.EE.01.EE0359.AY535659
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+>0708.CN.08.09YN072.HQ225812
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+>32A6.EE.06.A49.KM606637
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+>32G.EE.06.A45.KM606635
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+>A1B.US.10.DEURF10US008.KC473836
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+>A1BD.GB.16.DEURF16UK009.MN703144
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+>A1BG.SI.16.Sample68_SI555.MN736708
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+>A1C.IN.01.1579A.DQ083238
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+>A1C.IN.09.NARI_FLS_09_387.KC911635
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+>A1C.KE.05.05KE757760V5.KT022408
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+>A1C.KE.06.06KE161801V6.KT022413
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+>A1C.KE.10.DEURF10KE003.KF716471
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+>A1C.RW.06.DEURF06RW006.KU749428
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+>A1CD.KE.04.04KE956490V3.KT022398
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+>A1CDG.ZA.99.CM4_99ZACM4.AF411964
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+>A1D.CM.x.CMN05_5.KU168311
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+>A1D.KE.03.03KE543869V2.KT022385
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+>A1D.KE.04.04KE489686V2.KT022388
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+>A1D.KE.04.04KE719832V2.KT022392
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+>A1D.KE.04.04KE830543V3.KT022394
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+>A1D.KE.04.04KE880505V2.KT022396
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+>A1D.UG.07.p191947.JX236674
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+>A1D.UG.08.p191982.JX236675
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+>A1D.UG.09.DEURF09UG004.KF716481
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+>A1D.UG.09.DEURF09UG014.KP109491
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+>A1D.UG.09.DEURF09UG015.KP109492
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+>A1D.UG.10.DEURF10UG005.KF716487
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+>A1D.UG.10.DEURF10UG008.KF716490
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+>A1D.UG.10.DEURF10UG016.KP109493
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+>A1D.UG.11.DEURF11UG002.KP109497
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+>A1D.UG.11.DEURF11UG004.KF716484
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+>A1D.UG.11.DEURF11UG006.KF716485
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+>A1D.UG.15.E115410.MN694995
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+>A1F2.CM.11.CHU3903.KP718932
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+>A1G.CD.02.CG_0379_02V_NGSID7.KY392772
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+>A1GHU.GA.x.VI354.AF076474
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+>A1H.CM.08.867_10.KP718927
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+>A1H.CM.11.CHU2727.KP718933
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+>A1K.CM.07.280_10.KP718919
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+>A2C.ZM.90.ZAM184.U86780
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+>AC.KE.97.ML672.AY322191
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+>AC.ZA.04.04ZAPS204B1.DQ093606
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+>AGU.CM.06.770_8.MH705142
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+>AKU.US.x.L873.DQ886038
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+>AU.CD.87.PBS1342.MH705135
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+>BC.BR.01.01_BR_RGS45.GQ365651
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+>BC.BR.05.05_BR_NSP24.GQ365650
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+>BC.BR.07.DEURF07BR002.KC596068
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+>BC.BR.10.10BR_RJ009.KT427790
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+>BC.CN.00.HH069.AP005206
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+>BC.CN.05.05YNRL08sg.KC898976
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+>BC.CN.05.05YNRL09sg.KC898977
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+>BC.CN.05.05YNRL20sg.KC898978
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+>BC.CN.07.07CNYN335.KF835521
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+>BC.CN.07.07CNYN339.KF835525
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+>BC.CN.07.07CNYN340.KF835526
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+>BC.CN.07.07CNYN360.KF835539
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+>BC.CN.07.07CNYN361.KF835540
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gtggcg--------cccgaacagggac------------------ctgaaagcgaaag------------------------------------------taagaccagagga--------gatctctcgacgca-ggactcggcttgct---gaagtgcactcggcaagaggc-------------ga-g-ag--cggc-----ggctggtgagtacgcc-----------------------aattttatttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcaatattaagaggggaaaaattagataaatgggaaaaaattaggtta---agg------cca---gggggaaagaaacactatatgttaaaacacatagtatgggcaagcagggagctggaaagatttgcacttaaccctggccttttagagacatcagaaggctgtaagcaaataataaaacagctacaaccatct---cttcagacaggaacagaggaacttagatcattatacaacacagta---gcaactctctattgtgtacatgcagggatagaagtacaagacaccaaagaggccttagacaagatagaggaggaacaaaataaaattcag---------------------caaaaaacacagcaggcaaaagcaaag---------------gaggttggtgacggg------------------------------atg------------------------gtcagtcaaaattatcctata------------gtgcagaatctccaagggcaaatggtacatcagcccctatcccccagaactttaaatgcatgggtaaaagtggtagaagagaag------gcttttagcccagaagtaatacccatgtttacagcattatcagaaggagccaccccacaagatttaaacaccatgttaaatacagtaggggggcatcaa---gcagccatgcaaatg---ttaaaagat---accatcaatgaagaggctgcagaatgggatagattgcat---ccagtgcatgca---gggccagtggcaccaggccagatg---agagaaccaaggggaagtgacatagcaggaactactagtact---cttcaggagcaaataggatggatgaca---------aatactcca---cct---atc---ccagta---ggagaaatctataaaagatggataatcctgggattaaataaaatagtaagaatgtatagccctaccagcattctggacataaagcaagggccaaaggaaccctttagagactatgtagaccggttctttaaaactttaagagccgaacaagctacacaagatgtaaaaaattggatgacagaaaccttgttagtccagaatgcgaacccagattgtaagaccattttaagagcattaggaccaggggcttcattagaagaaatgatgacagcatgtcagggagtaggaggacctagccacaaa---gcaagagtgttggctgag------gcaatg---agccaatcaaac---------------------------agtgccata---atgatg------cagagaagcaat---------ttt---aaaggtcctaaaaga------attgttaaatgtttcaactgtggcaaggagggg---cacatagccagaaattgcagggcccctaggaaaaaaggctgttggaaatgtggaaaagaaggacaccaaatgaaagactgt---------------actgaaaggcaggctaattttttagggaaaatttggcc---ttcccacaa------ggg---gag---gccagggaatttcctccagagcagaccagagccaacagc------------------------------------------------------cccgccagc------agagagcttcaggtt------------cgagga---gac---aac---cccagc------------------------------tccgaa---------------gcaggaacc------------gaaagacag---------------------------gga------------------------agccttaacttccctcagatcactctttggcagcgaccccttgtctcaataaaagtagggggccagataaaagaggctctcttagacacaggagcagatgatacagtatta---gaagaa---ataaatttgccaggaaaatggaaaccaaaaatgataggaggaattggaggttttatcaaagtaagacaatat---gagcaaatatctatagaaatttgtggaaaaaaggctataggtacagtattagtgggacccacacctgtcaac---ataattggaagaaatctgctgacccagcttggatgcacactaaattttccaatcagtcccattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaggttaaacaa---tggccattgacagaagag---aaaataaaagcattaacagcaatttgtgag------gaaatggagaaggaaggaaaaattacaaaa---attgggcct---gacaatccatataacactccaatatttgccataaaaaagaaagacagt------actaagtggagaaaattagtagatttcagggaactcaataaaagaactcaagatttttgggaa---gttcaa------ttg---ggaata---------------------------ccacacccagcagggttaaaaaagaaa---aaa------tcagtaacagtcctggatgtgggtgatgcatat---ttctcagttcctttagataaagacttcaggaagtatactgcatttaccatacctagtgtaaacaatgagacaccaggaattagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaatgtagcatgacaaaaatcttagagccttttagaaaacaaaatccagacatagttatctatcaatacatggatgatttgtatgtaggatctgacttagagatagggcagcatagaacaaaaatagaggaactgagagaacatttgttgaagtggggatttaccacaccagacaagaaacatcagaaagaacctccatttctttggatggggtatgaactccatcctgacaaatggacagtacagcctatacagctaccagaa---aaagat---agctggactgtcaatgatatacaaaagttagtgggaaaattaaactgggcaagtcagatctatcctggaattaaagtaaggcagctttgtaaactccttaggggggctaaagcactaacagaaatagtaccactaactgaagaagcagaattagaattggcagaaaacagggaaattctaaaagagccagtacatggggtatattatgacccatcaaaagacttgatagctgaaatacagaaacaagggcaggaccaatggacatatcaaatttaccaagaaccattcaaaaatctaaagacagggaagtatgcaaaaatg---aggactgcccacacgaatgatgta------aaacaattaactgaggctgtgcagaaaatagccatggaaagcatagtaatatggggaaag---actcctaaattcagattacccatccaaaaagaaatatgggagacatggtggacagactattggcaagccacctggattcctgagtgggaatttgttaatacccctcccttagtaaaattatggtaccagttggaaaaagatcccatagcaggagcagaaactttctatgtagatggagcagctaatagggagactaaaataggaaaagcagggtatgttactgacagaggaaggaaaaaa---gttgtttctctaactgaaacaacaaatcagaggacagagttgcaagcaatttgtatagctttgcaagattcaggatcagaag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+>BC.CN.07.07CNYN367.KF835544
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+>BC.CN.07.07YNLC22sg.KC899007
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+>BC.CN.07.309.HM776938
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+>BC.CN.07.cq070084.KF250381
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+>BC.CN.07.gd070112.KF250382
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+>BC.CN.08.08YN065.GU362013
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+>BC.CN.09.09YNLC216036sg.KC898988
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+>BC.CN.09.09YNLC492sg.KC898989
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+>BC.CN.09.09YNRL215025sg.KC899010
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+>BC.CN.09.09YNYJ479sg.KC899015
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+>BC.CN.10.JL100091.KF011493
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+>BC.CN.12.DH24.KF250406
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+>BC.CN.12.DH36.KF250410
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+>BC.CN.14.XC2014EU20.KU886698
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+>BC.MM.99.mIDU103.AB097873
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+>BC.SE.13.087SE.MF373189
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+>BF1.AR.12.DEURF12AR009.KY658687
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+>BF1.AR.14.DEURF14AR011.MH078535
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+>BF1.BR.00.BREPM13853.DQ085875
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+>BF1.BR.01.01BR042.DQ358799
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+>BF1.BR.01.01BR226.DQ358803
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+>BF1.BR.01.01BR323.DQ358804
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+>BF1.BR.02.02BR005.DQ358806
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+>BF1.BR.02.02BR006.DQ358807
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+>BF1.BR.02.02BR034.DQ358812
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+>BF1.BR.02.02BRRJSB167.MG365770
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+>BF1.BR.03.03BR2019.JN692448
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+>BF1.BR.03.BREPM1026.EF637055
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+>BF1.BR.04.04BR1067.JN692456
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+>BF1.BR.05.0008SP.JF804805
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+>BF1.BR.05.0341RI.JF804808
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+>BF1.BR.05.0736SV.JF804813
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+>BF1.BR.06.06BR_FPS561.HM026455
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+>BF1.BR.09.09BRRJRDS205.MG365769
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+>BF1.BR.10.10BR_MG003.KJ671533
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+>BF1.BR.10.10BR_MG034.KJ849802
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+>BF1.BR.10.10BR_PE005.KT427746
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+>BF1.BR.10.10BR_RJ014.KT427789
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+>BF1.BR.10.10BR_RJ075.KT427651
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+>BF1.BR.10.10BR_SP018.KT427820
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+>BF1.BR.10.10BR_SP054.KT427801
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+>BF1.BR.99.99BRRJSB067.MG365765
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+>BF1.BR.99.BREPM107.AY771588
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+>BF1.BR.99.BREPM108.AY771589
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+>BF1.BR.99.BREPM11931.DQ085869
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+>BF1.ES.08.DEURF08ES008.KU749408
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+>BF1.ES.09.DEMBF09ES003.JX140660
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+>BF1.ES.09.DEMBF09ES006.JX140661
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+>BF1G.MO.05.MO108.GU207884
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+>CD.MW.08.CH492.PL.031108.A2.7.KY112292
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+>CD.NP.11.11NP079.KU341727
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+>CD.SE.08.029SE.MF373143
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+>CU.ZA.13.DEURF13ZA135.KU749418
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+>DG.CM.06.876_14.KP718916
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+>DG.KE.06.06KECst_014.FJ623495
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+>FK.CD.87.P3844.MH705156
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+>U.CD.02.CG_0059_01_NGSID8.KY392773
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+>U.CD.x.BCF_Kita.AB485665
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+>U.CM.07.469_66.KP718920
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+>U.NL.95.U_NL_95_H10986_D1.EF029066
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+>U.SI.11.Sample34_SI300.MN736701
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------g-cctgc-tagag------a-acccactg-c-tt-aa------gcctcaa-taaagcttg-cc-tt-gagtgc-ttc--aa-g-----ta-gtgt-gtgcccgtctg-t-tg--------------tgtgact---ctggt-a---------------actagagatc-------cctcagaccact-ctag-a-tagtat-aaaaa-tctctagcagtggcg--------cccgaacagggac------------------ttgaaagcgaaag---------------------ttaacagggactcgaaagcgaaagttccagagaa--------gttctctcgacgca-ggactcggcttgct---gaggtgcacgcagcaagaggc-------------ga-g-ag--cggc-----gactggtgagtacgcc------------------------aaattttttgact----------agcgga-gg---------ctaga-----------a--g--------------ga-g-a-g--ag--------------------------atgggtgcgagagcgtcagtattaagcgggggaaaattagatgcatgggaaagaattcggctg---agg------cca---gggggaaagaaaaaatatagactgaaacatttagtatgggcaagcagggagctggaaagatttgcacttaaccctagcctcttagacagcgcagaaggttgtcagcaaataatgggacaattacaatcagct---ctcgggacaggaacagaagaacttagatcattatttaatacagta---gcaaccctctattgtgtacatcaaaggatagagataaaagacaccaaggaagctttagataaaatagaggaactgcaaaataagagcaag------------------------caaaaggcacagcaggcagcagag---------------------aaaacagga------------------gac---cacaaccag------------------------gtcagtcaaaattaccctcta------------gtgcagaatgcacaagggcaaatgatacaccagtccatgtcacctaggactttaaatgcatgggtaaaagtaatagaagaaaag------gctttcagcccagaagtaatacccatgttttcagcattgtcagaaggagccaccccacaagatttaaatatgatgctgaacatagtaggggggcaccaa---gcagctatgcaaatg---ctaaaggat---actatcaatgaagaagctgcagagtgggataggttacat---ccacaacaggca---gggccttatccaccaggccaaatg---agagaaccaaggggaagtgacatagcaggaacaactagtacc---cttcaagaacaaataggatggatgaca---------ggtaaccca---cct---gtc---ccagtg---ggagacatctatagaaggtggataatcctgggcttaaataagatagtaagaatgtatagccctgtcagcattttggacataaaacaagggccaaaagaacccttcagagattatgtagacaggttttttaaaactttgagagctgagcaagccacacaggatgtaaaaaattggatgacagacaccttgttggtccaaaatgcgaatccagattgtaagaacatcctaagagcattaggaccaggagctacactagaagaaatgatgacagcatgccaaggagtgggaggacctggccacaaa---gcaagagttttagctgag------gcaatg---agccaggtatca------------------------aacgcagccgta---atgatg------caaaaaggcaat---------ttt---aagggcccgaaaaga------aatattaagtgtttcaactgtggtaaggaagga---catctagccagaaattgcagggcccctaggaaaaagggctgttggaaatgtggaaaagagggacatcaaatgaaagactgc---------------acagagagacaggctaattttttagggagaatttggcc---ttccaacaa------agg---aag---gccaggaaattttctccagagcaggccagagccaaccgc------------------------------------------------------cccaccagc------agagagcttcgggtt------------cggggaggagat---aac---cccctc------------------------------ccagaa---------------gcaggagcc------------gaaggagaa------------------------ggagga------------gctgta------tcccttagcttccctcaaatcactctttggcaacgaccccttgtcacaataaaaatagcggggcagctgagggaagctctattggatacaggagcagatgatacagtatta---gcagaa---atagatttgccaggaagatggaaaccaaaaatgatagggggaattggaggatttatcaaagtaaaacagtat---gatcaaatacttatagaaattgaagggaaaaaggctatagggacagtactagtaggacctacacctatcaac---ataattggaagaaatatgttgactcagattggttgtactttaaattttccaattagtcctattgagactgtcccagtaaaattaaagccaggaatggatggcccaaagattaaacaa---tggccattgacagaagag---aaaataaaggcattaacagaaatttgtaca------gacatggaaaaggaaggaaaaatttcaaga---attgggcct---gaaaatccatacaacactccaatatttgccataaagaaaaaagatagt------actaaatggagaaaattggtagatttcagagagcttaataaaagaactcaagacttctgggag---gtccaa------tta---ggcata---------------------------cctcaccctgcggggttaaaaaagaaa---aaa------tcagtaacagtactggatgtgggggatgcatat---ttttcagtccctctagacgaaaatttcagaaagtatactgcattcactatacctagtataaataatgagacaccagggattagatatcagtacaatgtgcttccccagggatggaaaggatcaccagcaatatttcagagtagcatgataaaaatcttagaaccctttagaacaaaaaatccagaaatagtgatctaccagtacatggatgatttatatgtaggatctgacttagaaataggacagcatagagcaaaagtagaggagttaagagagcacctactgaaatggggatttactacaccagataaaaaacatcagaaagagcctccatttctttggatgggatatgagctccatcctgacaaatggacagtacaacctatacagttgccagac---aaggaa---tgttggactgtcaatgatatacaaaaattagtgggaaaactaaattgggcaagccagatatatccagggattaaggtaaaacacttatgtagactccttagaggaacaaaagcactaacagatataataccattgactgcagaagcagaattggaattggcagagaacagggaaattctaaaagaaccagtacatggggtatattatgacccatcaaaagagttaatagcagaagtacaaaaacaagggctagaccaatggacatatcaaatatatcaagagccattcaaaaacctgaaaacagggaaatatgcaaaaaga---aggactgcccacactaatgatgta------aggcaactagcagaagtgacacaaaagatatccatggaaagcatagtgatatggggaaaa---attcctaaatttagattacccatacaaaaagaaacatgggacacatggtggacagattattggcaggccacctggatccctgaatgggagtttgttaataccccacctctggtaaagttatggtatcaattagaaacagaacccataccaggggcagaaacttactatgtagatggggcagctaatagggaaacaaaattaggaaaagcaggatatgttactgacagaggaaaacaaaaa---attatcaccatgcaggaaacaacaaaccaaaaggctgaattacaagcaattcagttagctttgcaggactcaggatcagaag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tcttgggagcagca---ggaagcactatgggcgcagcgtca---ataacgctgacggtacaagcc---aga------caa---ttattg---tctggcatagtgcaacagcag---agcaatctg---ctgagggctatagaggctcaacagcatatgttgaaacttacagtctggggcataaaacagctccag---gcaagagtcctggctatagaaagatacctaaaagatcaacagctcctaggaatttggggatgctctggaaaactcatctgccccactaatgtgccttggaattct---agc---tgg------------------------------------agtaataagtctcaggatgaaatatgg---------gaa---aacatgacatggctgcaa---tgg---gag-aaagaaattagtaattacacacagacaatatatgatctaattgaaaaatcgcag-aaccagcaggaa-aagaatgaacaggatttattggcattggacaaatgggcaagtctgtggaattggtttgacataacaagatggctgtggtatata-aaaatatttataatgatagttggaggcttaataggttta-agaataatttttgctgtgctttctatagtaaggagagttaggcagggatactcacctttatca---ttccag---acccttacccaccac------cagagggaa------ccagacagg------cccggagaaatcgaaagagaaggtggagagcaagacagaggcagatccgtgcgattagtgagcggattcttagcacttgcctgggacgatctacggagcctgtgcctcttcagctac---caccgcttgagagacttcatattgattgtagcgaggactgtggaa---ctt---ctg---ggacacaacagtctcaagggactgagg------------------------ctggggtgg------gaaggcctcaac---tacctg---------tggaatcttctggtgtattggattagggaactgaagattagtgct--actactttgctcgatactatagcaatagcagtagctggg-tggacagatagggttatagagctaggacaaaggcttggaaga------ggtatcctccacatacccaga---agaatcaggcagggctttgaaagattt------ttg-------cta---taa--------------------------------------catgggaggcaagtggtcaaaa------agcagcata---gtg---ggatggccagatgtaagggaaagaataaagcaaactccc---------------------------------------------------------ctaccagca------------------------------gcagcaggagtaggacca---gtatctcaagatttagataaacatggagcaatcaccagtagtaat------gttaatcatgctagt---tgtgcctggctggaagca---------caagagaac---------gag------gaggtgggctttccagtcagacctcaggtacccttaagaccaatgacttataagggagctttt------gatcttagcttctttttaaaagaaaaggggggactg---gatgggctaatttactctaagaaaagacaagagatc---------cttgatctttgggtctataataca-caa---ggcttcttccctgattggcaa---aactacacaccagggccagggaccagatacccattatgttttggatggtgcttcaagttagtaccagttgacccaagagaagtagaagag------gccagtgaagga------gagaacaactgcctgttacaccccatgtgccagcatggagcagatgatgaa---gaaaga---gaagtgttaatgtggaagtttgacagtgcgctggca-cgaaaacacatagcccgagagatgcat---ccggagttc------------------------tacaaagactgctgac-----------------------------------------aaagaagtt-------------------------tctaaca----------------------------------------aggactt-cc----------------gctg---------------------------------------gggactttcc--------------------------------------------------------------------------------aggggaggt------------gtggcg-tgggtggagct-----------gggg-agtg-gc-taa--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>U.SI.12.Sample37_SI324.MN736702
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+>O.CM.03.296.MH705148
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+>O.CM.06.20_02.MH705150
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+>O.CM.91.MVP5180.L20571
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+>O.CM.94.LA50YBF16.KU168293
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+>O.CM.95.LA29YBF26.KU168281
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+>O.CM.96.LA51YBF35.KU168294
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+>O.ES.01.Read25_HIV_GroupO.KX228804
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+>O.FR.03.LA32RBF140.KU168284
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+>O.FR.06.RBF206.KY112585
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+>O.FR.95.LA47BCF09.KU168290
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+>O.FR.95.LA48BCF13.KU168291
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+>O.FR.98.LA53BCF109.KU168296
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+>O.FR.99.LA54BCF120.KU168297
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+>O.SN.99.99SE_MP1299.AJ302646
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+>N.CM.95.YBF30.AJ006022
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+>CPZ.CD.06.BF1167.JQ866001
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+>CPZ.CM.05.SIVcpzEK505.DQ373065
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+>CPZ.CM.05.SIVcpzLB7.DQ373064
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+>CPZ.CM.05.SIVcpzMT145.DQ373066
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+>CPZ.GA.88.SIVcpzGAB2.AF382828
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+>CPZ.TZ.02.TAN3_1.DQ374658
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+>CPZ.TZ.06.SIVcpzTAN13.JQ768416
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+>CPZ.TZ.09.UG38.JN091690
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+>GOR.CM.07.SIVgor2139_287.FJ424866
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diff --git a/bin/config.sh b/bin/config.sh
index a8f7991..b055dab 100644
--- a/bin/config.sh
+++ b/bin/config.sh
@@ -252,6 +252,21 @@ KeepPreMappingReads=false
 MaxContigGappiness=0.05
 MinContigHitFrac=0.9
 
+# CodonCorrection.sh variables:
+virulign=~/VIRULIGN/virulign # testing - set to a more 'default' variable before finalising CC.sh
+# Shall we codon-correct the shiver output before remapping?
+CodonCorrect=true
+# The genes that can be analysed by VIRULIGN:
+genes="GAG POL VIF VPR VPU ENV NEF"
+# Which data should be output by VIRULIGN? Separated by ',' and enclosed by double quotes (see CodonCorrection.sh help for more details)
+VirulignOptions="Nucleotides,Mutations,AminoAcids"
+# Which genes should be corrected? Separated by ',' and enclosed by double quotes (see CodonCorrection.sh help for more details)
+GenesToCorrect="all"
+# Shall we delete temporary files within the CodonCorrection.sh output? 
+CC_DeleteTemp=false
+# Should key messages in the CodonCorrection output be printed in colour?
+CC_EnableColours=true
+
 # Suffixes we'll append to the sample ID for output files.
 # If you change the extension (whatever follows the dot) you might break
 # something.
diff --git a/bin/shiver_funcs.sh b/bin/shiver_funcs.sh
index 560f394..4b20fe0 100644
--- a/bin/shiver_funcs.sh
+++ b/bin/shiver_funcs.sh
@@ -27,6 +27,8 @@ Code_PrintSeqLengths="$ToolsDir/PrintSeqLengths.py"
 Code_AddSNPsToSeqs="$ToolsDir/AddAllPossibleSNPsToSeqs.py"
 Code_KeepBestLinesInDataFile="$ToolsDir/KeepBestLinesInDataFile.py"
 Code_ConvertFastqToFasta="$ToolsDir/ConvertFastqToFasta.py"
+Code_CodonCorrectionInit="$ToolsDir/CodonCorrectionInit.sh"
+Code_CodonCorrection="$ToolsDir/CodonCorrection.sh"
 
 # Only needed if GiveHXB2coords is set to true in the config file
 HXB2file=$(dirname "$ThisDir")'/data/external/B.FR.83.HXB2_LAI_IIIB_BRU.K03455.fasta'
diff --git a/bin/shiver_init.sh b/bin/shiver_init.sh
index 591bcb3..5f05299 100755
--- a/bin/shiver_init.sh
+++ b/bin/shiver_init.sh
@@ -147,3 +147,18 @@ mkdir -p "$IndividualRefDir" || \
 exit 1; }
 "$python" "$Code_SplitFasta" -G "$RefAlignment" "$IndividualRefDir" || { echo "Problem" \
 "splitting $RefAlignment into one file per sequence. Quitting." >&2 ; exit 1; }
+
+# Make the CodonCorrection init directory
+# NB This assumes that the /CodonCorrectionReferences is part of shiver to avoid changing the init arguments for now.
+# If this is not the case, then the reference file and gene coordinates will need to be supplied as an init argument.
+if [[ "$CodonCorrect" == "true" ]]; then
+  CC_RefFile="$ThisDir"/'CodonCorrectionReferences/HIV1_ALL_2020_genome_DNA_no_ambiguity_only_annotated_aligned_no_gap_columns_aligned.fasta'
+  CC_GeneCoords="$ThisDir"/'CodonCorrectionReferences/AnnotatableGenePositions.txt'
+  CC_Init="$OutDir"/'CodonCorrectionInit'
+  "$Code_CodonCorrectionInit" "$CC_RefFile" "$CC_Init" "$CC_GeneCoords" || \
+  { echo "Problem initialising CodonCorrection. Quitting." >&2 ; exit 1; }
+fi
+
+
+
+
diff --git a/bin/shiver_map_reads.sh b/bin/shiver_map_reads.sh
index 348ebba..5e45a12 100755
--- a/bin/shiver_map_reads.sh
+++ b/bin/shiver_map_reads.sh
@@ -745,4 +745,12 @@ if [[ "$remap" == "true" ]]; then
     { echo 'Problem remapping to the consensus from the first round of mapping.'\
     'Quitting.' >&2 ; exit 1 ; }
   fi
+
+  # Codon-correct the round 2 consensus
+  CC_Init="$InitDir"/'CodonCorrectionInit'
+  CC_Output=./'CodonCorrection'
+  CC_Consensus="$NewSID"'_consensus_MinCov_'"$MinCov1"'_'"$MinCov2.fasta"
+  "$Code_CodonCorrection" "$CC_Consensus" "$virulign" "$CC_Init" "$VirulignOptions" "$GenesToCorrect" "$CC_Output" || \
+  { echo 'Problem codon-correcting the consensus before remapping. Quitting.' >&2 ; exit 1 ; }
+
 fi
\ No newline at end of file
diff --git a/bin/tools/CC_Python_funcs.py b/bin/tools/CC_Python_funcs.py
new file mode 100644
index 0000000..5e9bad2
--- /dev/null
+++ b/bin/tools/CC_Python_funcs.py
@@ -0,0 +1,634 @@
+#!/usr/bin/env python
+
+import sys
+import os
+from Bio import AlignIO
+from Bio import SeqIO
+import csv
+import argparse
+from AuxiliaryFunctions import ungap
+
+HelpMessage = "Script containing all the required python functions for Codon_Correction.sh. Each function is called with the relevant \
+optional arguments in the CodonCorrection script and init script."
+
+# Set up arguments
+parser = argparse.ArgumentParser(description=HelpMessage)
+parser.add_argument('FunctionName')
+parser.add_argument('--InitDir', help='The location chosen for the init directory')
+parser.add_argument('--GeneCoordInfo', help='Gene coordinate information file') # be more descriptive of format
+parser.add_argument('--GenomeFile', help='Fasta file of all the references as complete genomes (as opposed to individual genes).')
+parser.add_argument('--AlignmentFile', help='Fasta file containing the HXB2 sequence included with shiver aligned to the sample.')
+parser.add_argument('--SingleSeq', help='Set to true or false in CC.sh depending on number of sequences in the sample file.')
+parser.add_argument('--ReferenceName', help='Name of the reference that BLASTs to the gene')
+parser.add_argument('--Gene', help='The current gene being processed')
+parser.add_argument('--AlignmentToRef', help='Fasta file containing the reference sequence for each gene aligned to the sample genome.')
+parser.add_argument('--OutputFile', help='The name of the output fasta file to write to')
+parser.add_argument('--InputFile', help='The name of the input fasta file')
+parser.add_argument('--SequenceNumber', help='The number of the sequence needed to extract (1-based)')
+parser.add_argument('--OutputCSV', help='The name of the output .CSV file to write to')
+parser.add_argument('--SequenceName', help='Name of the sample sequence')
+parser.add_argument('--ExtractedGeneFile', help='The name of the sample gene file extracted after alignment with the BLAST reference')
+args = parser.parse_args()
+
+# Select function to call
+function_name = args.FunctionName
+
+# MakeReferenceDatabase uses the whole genome reference file to  extract individual genes to a separate fasta file based on gene type
+def MakeReferenceDatabase(InitDir, GeneCoordInfo, GenomeFile):
+  print('Now extracting reference genes from database')
+  # Parse the whole genome sequences
+  try:
+    with open(GenomeFile, 'r') as genome_handle:
+      genome_records = SeqIO.to_dict(SeqIO.parse(genome_handle, "fasta"))
+  except IOError:
+    print(('Error: Could not open file {}'.format(GenomeFile)))
+    raise
+  except ValueError:
+    print(('Error: File {} is not in the expected format'.format(GenomeFile)))
+    raise
+
+  # Assign gene info per sequence in coordinates file
+  gene_loci = {}
+  try:
+    with open(GeneCoordInfo, 'r') as file:
+      next(file)
+      for line in file:
+        gene_info = line.strip().split(',')
+        if len(gene_info) != 15:
+          print('Error: The gene coordinate file has an unexpected number of fields. Quitting.')
+          exit(1)
+        
+        CoordRefName = gene_info[0]
+        if CoordRefName in gene_loci:
+          print('Error: encountered reference', CoordRefName,
+          'a second time in', GeneCoordInfo, file=sys.stderr)
+          exit(1)
+        
+        gene_loci[CoordRefName] = {
+          # Gene: (gene_start, gene_end)
+          'GAG': (int(gene_info[1]), int(gene_info[2])),
+          'POL': (int(gene_info[3]), int(gene_info[4])),
+          'VIF': (int(gene_info[5]), int(gene_info[6])),
+          'VPR': (int(gene_info[7]), int(gene_info[8])),
+          'VPU': (int(gene_info[9]), int(gene_info[10])),
+          'ENV': (int(gene_info[11]), int(gene_info[12])),
+          'NEF': (int(gene_info[13]), int(gene_info[14]))
+        }
+        
+        # Check start & end coords are OK
+        for gene, (start, end) in gene_loci[CoordRefName].items():
+          if end < start:
+            print("Error: for reference", CoordRefName + ", gene", gene,
+            "has an end position before its start position.", file=sys.stderr)
+            exit(1)
+          if (end - start + 1) % 3 != 0:
+            print("Error: for reference", CoordRefName + ", gene", gene,
+            "has length", end - start + 1, "which is not a multiple of 3. This",
+            "is not compatible with use for codon correction.",
+            file=sys.stderr)
+            exit(1)
+        
+        # Find matching genome sequence
+        if CoordRefName in genome_records:
+          GenomeSeq = genome_records[CoordRefName].seq
+        else:
+          print(('Sequence {} not found in genome file. Quitting'.format(CoordRefName)))
+          exit(1)
+
+        # Extract reference sequence for each gene
+        for gene_class, (gene_start, gene_end) in list(gene_loci[CoordRefName].items()):
+          OutputFile = os.path.join(InitDir, 'ReferenceGenes_{}.fasta'.format(gene_class))
+          try:
+            with open(OutputFile, 'a') as output_file:
+              if gene_start is not None and gene_end is not None:
+                ref_pos = 0
+                ref_start = 0
+                ref_end = 0
+                for i, base in enumerate(GenomeSeq):
+                  if base != '-':
+                    ref_pos += 1
+                  if ref_pos == gene_start:
+                    ref_start = i
+                  if ref_pos == gene_end:
+                    ref_end = i
+                    gene_sequence = ungap(GenomeSeq[ref_start:ref_end + 1])
+                    output_file.write('>' + CoordRefName + '_' + gene_class + '\n' + str(gene_sequence) + '\n')    
+                    break
+          except IOError:
+            print(('Error: Could not open file {}'.format(OutputFile)))
+            raise
+          except ValueError:
+            print(('Error: File {} is not in the expected format'.format(OutputFile)))
+            raise
+    missing_refs = [ref_ for ref_ in genome_records.keys() if not ref_ in \
+    gene_loci.keys()]
+    if len(missing_refs) > 0:
+      print("Warning: some references have a sequence in ", GenomeFile,
+      " but their gene coordinates are not given in ", GeneCoordInfo, 
+      ". They will not be used for codon correction. These references are: ",
+      ' '.join(missing_refs), sep='', file=sys.stderr)
+  except IOError:
+    print(('Error: Could not open file {}'.format(GeneCoordInfo)))
+    raise
+  except ValueError:
+    print(('Error: File {} is not in the expected format'.format(GeneCoordInfo)))
+    raise
+  return 0
+
+# Call MakeReferenceDatabase
+if function_name == 'MakeReferenceDatabase':
+  MakeReferenceDatabase(args.InitDir, args.GeneCoordInfo, args.GenomeFile)
+
+# ExtractWithHXB2 uses a set of predetermined HXB2 coordinates to extract genes from the sample file. Using a set reference
+# will reduce accuracy of results, but the extracted genes are only used to BLASTn to a closer reference which will then
+# be used to extract the final sample gene sequences used for VIRULIGN
+def ExtractWithHXB2(AlignmentFile, SingleSeq):
+
+  SingleSequence_check = SingleSeq
+  RefSequenceNumber = 0
+  if SingleSequence_check == 'true':
+    RefSequenceNumber = 1
+  else:
+    RefSequenceNumber = 2
+
+  # Assign variables
+  HXB2Alignment = AlignIO.read(AlignmentFile, 'fasta')
+  SequenceName = HXB2Alignment[0].id
+  RefSequenceLength = len(HXB2Alignment[RefSequenceNumber])
+
+  # Extract gene coordinates from the reference file - for HXB2 these are set to predetermined values
+  hxb2_loci = {
+    # Gene: (gene_start, gene_end)
+    'GAG': (int(790), int(2292)),
+    'POL': (int(2253), int(5096)),
+    'VIF': (int(5041), int(5619)),
+    'VPR': (int(5559), int(5850)),
+    'VPU': (int(6062), int(6310)),
+    'ENV': (int(6225), int(8795)),
+    'NEF': (int(8797), int(9168))
+  }
+
+  # Gene extraction for sample sequence
+  if hxb2_loci:
+    for gene, (gene_start, gene_end) in list(hxb2_loci.items()):
+      OutputFile = "temp_preBLAST_Sample_Gene_{}.fasta".format(gene) # is this correct?
+      try:
+        with open(OutputFile, 'w') as output_file:
+          if gene_start is not None and gene_end is not None:
+            # Iterate over the sequence to determine gene coordinates of the sample sequence
+            consensus_start = 0
+            consensus_end = 0
+            sequence_pos = 0
+            for i in range(RefSequenceLength): # try ennumerate as above, and/or set sequence to a variable
+              if HXB2Alignment[RefSequenceNumber][i] != '-':
+                sequence_pos += 1
+              if sequence_pos == gene_start:
+                consensus_start = i
+              if sequence_pos == gene_end: 
+                consensus_end = i
+                break
+
+            # Write the gene sequence to file unless it contains '?'
+            if consensus_start is not None and consensus_end is not None:
+              gene_sequence = ungap(HXB2Alignment[0].seq[consensus_start:consensus_end + 1])
+              if '?' in gene_sequence:
+                print(('Gene {} contains \'?\' characters indicating missing coverage. Skipping.'.format(gene)))
+                with open('MissingCoverage.txt', 'a') as file:
+                  file.write(SequenceName + '_' + gene + '\n')
+                continue
+              else:
+                output_file.write('>' + SequenceName + '_' + gene + '\n' + str(gene_sequence) + '\n')
+      except IOError:
+        print(('Error: Could not open file {}'.format(OutputFile)))
+        raise
+      except ValueError:
+        print(('Error: File {} is not in the expected format'.format(OutputFile)))
+        raise
+        
+  return 0
+
+
+# Call ExtractWithHXB2
+if function_name == 'ExtractWithHXB2':
+  ExtractWithHXB2(args.AlignmentFile, args.SingleSeq)
+
+# ExtractRefFromFasta takes the single whole genome sequence out of the full reference fasta
+def ExtractRefFromFasta(ReferenceName, GenomeFile, Gene):
+  output_ref = 'temp_Reference_Genome_' + Gene + '.fasta' 
+  found = False
+  try:
+    with open(output_ref, 'w') as file:
+      for record in SeqIO.parse(GenomeFile, 'fasta'):
+        if record.id == ReferenceName:
+          SeqIO.write(record, file, 'fasta')
+          found = True
+          break
+  except IOError:
+    print(('Error: Could not open file {}'.format(GenomeFile)))
+    raise
+  except ValueError:
+    print(('Error: File {} is not in the expected format'.format(GenomeFile)))
+    raise
+
+  if not found:
+    print(('Reference sequence {} was not found within the provided reference file {}.'.format(ReferenceName, GenomeFile)))
+  
+  return 0
+
+# Call ExtractRefFromFasta
+if function_name == 'ExtractRefFromFasta':
+  ExtractRefFromFasta(args.ReferenceName, args.GenomeFile, args.Gene)
+
+def ExtractRefandSample(AlignmentToRef, SingleSeq, ReferenceName, GeneCoordInfo, Gene):
+
+  SingleSequence_check = SingleSeq
+  RefSequenceNumber = 0
+  if SingleSequence_check == 'true':
+    RefSequenceNumber = 1
+  else:
+    RefSequenceNumber = 2
+
+  # Assign variables
+  ReferenceAlignment = AlignIO.read(AlignmentToRef, 'fasta')
+  SequenceName = ReferenceAlignment[0].id
+  RefSequenceLength = len(ReferenceAlignment[RefSequenceNumber])
+  output_file_name = '{}_GenesExtracted.fasta'.format(SequenceName)
+  ref_output_file_name = '{}_Reference_GenesExtracted.fasta'.format(SequenceName) # Could be changed to use ReferenceName if that's clearer
+
+  # Extract gene coordinates from the reference file
+  try:
+    with open(GeneCoordInfo, 'r') as file:
+      for line in file:
+        gene_info = line.strip().split(',')
+        if gene_info[0] == ReferenceName:
+          # Identify gene and select corresponding gene info coordinates
+          if Gene == "GAG":
+            gene_start = int(gene_info[1])
+            gene_end = int(gene_info[2])
+          elif Gene == "POL":
+            gene_start = int(gene_info[3])
+            gene_end = int(gene_info[4])
+          elif Gene == "VIF":
+            gene_start = int(gene_info[5])
+            gene_end = int(gene_info[6])
+          elif Gene == "VPR":
+            gene_start = int(gene_info[7])
+            gene_end = int(gene_info[8])
+          elif Gene == "VPU":
+            gene_start = int(gene_info[9])
+            gene_end = int(gene_info[10])
+          elif Gene == "ENV":
+            gene_start = int(gene_info[11])
+            gene_end = int(gene_info[12])
+          elif Gene == "NEF":
+            gene_start = int(gene_info[13])
+            gene_end = int(gene_info[14])
+          else:
+            print('Could not match gene name to any of the expected inputs. Quitting')
+            exit(1)
+          break
+        else:
+          continue
+      if gene_start is None or gene_end is None:
+        print('Could not match the reference sequence to any within the reference file. Quitting.')
+        exit(1)
+  except IOError:
+    print(('Error: Could not open file {}'.format(GeneCoordInfo)))
+    raise
+  except ValueError:
+    print(('Error: File {} is not in the expected format'.format(GeneCoordInfo)))
+    raise
+
+  # Gene extraction for reference sequence
+  try:
+    with open(ref_output_file_name, 'a') as output_file:
+      ref_pos = 0
+      ref_start = 0
+      ref_end = 0
+      for i in range(RefSequenceLength):
+        if ReferenceAlignment[RefSequenceNumber][i] != '-':
+          ref_pos += 1
+        if ref_pos == gene_start:
+          ref_start = i
+        if ref_pos == gene_end:
+          ref_end = i
+          break
+
+      if ref_start is not None and ref_end is not None:
+        # Write the reference sequence to a file
+        reference_sequence = ungap(ReferenceAlignment[RefSequenceNumber].seq[ref_start:ref_end + 1])
+        output_file.write('>' + ReferenceAlignment[RefSequenceNumber].id + '_' + Gene + '\n' + str(reference_sequence) + '\n')
+      else:
+        print('Unable to extract the reference coordinates. Quitting.')
+        exit(1)
+  except IOError:
+    print(('Error: Could not open file {}'.format(ref_output_file_name)))
+    raise
+  except ValueError:
+    print(('Error: File {} is not in the expected format'.format(ref_output_file_name)))
+    raise
+
+  # Gene extraction for sample sequence
+  try:
+    with open(output_file_name, 'a') as output_file:
+      # Iterate over the sequence to determine gene coordinates of the sample sequence
+      consensus_start = None
+      consensus_end = None
+      sequence_pos = 0
+      indel_difference = 0
+      for i in range(RefSequenceLength):
+        if ReferenceAlignment[RefSequenceNumber][i] != '-':
+          sequence_pos += 1
+        if sequence_pos == gene_start:
+          consensus_start = i
+        if sequence_pos == gene_end: 
+          consensus_end = i
+          break
+
+      if consensus_start is not None and consensus_end is not None:
+        # Calculate indel size
+        gene_sequence_gapped = ReferenceAlignment[0].seq[consensus_start:consensus_end + 1]
+        sample_gaps = gene_sequence_gapped.count('-')
+        indel_difference =  (consensus_end + 1 - consensus_start - sample_gaps) - (gene_end + 1 - gene_start)
+        if indel_difference != 0:
+          print(('Change in length of {} in {}_{} relative to the reference'.format(indel_difference, SequenceName, Gene))) # This can be removed if not useful, it was mostly used when I was debugging length issues
+
+        # Write the gene sequence to file unless it contains '?'
+        gene_sequence = ungap(ReferenceAlignment[0].seq[consensus_start:consensus_end + 1])
+        if '?' in gene_sequence:
+          print(('Gene {} contains \'?\' characters indicating missing coverage. Skipping.'.format(Gene)))
+          with open('MissingCoverage.txt', 'a') as file:
+            file.write(SequenceName + '_' + Gene + '\n')
+        else:
+          output_file.write('>' + SequenceName + '_' + Gene + '\n' + str(gene_sequence) + '\n')
+
+        # Write the sample gene start to a file for later use in indel position calculation
+        gene_start_full_genome = len(ungap(ReferenceAlignment[0].seq[0:consensus_start + 1]))
+        with open('temp_GeneStarts.csv', 'a', newline='') as csvfile:
+          fieldnames = ['Sequence', 'Gene', 'GeneStart']
+          writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
+          if csvfile.tell() == 0:
+            writer.writeheader()
+          writer.writerow({'Sequence': SequenceName, 'Gene': Gene, 'GeneStart': gene_start_full_genome})
+      else:
+        print(('Unable to extract sample coordinates for {}.'.format(Gene))) 
+  except IOError:
+    print(('Error: Could not open file {}'.format(output_file_name)))
+    raise
+  except ValueError:
+    print(('Error: File {} is not in the expected format'.format(output_file_name)))
+    raise
+
+  # Extract the sample sequences to individual fastas for VIRULIGN processing
+  multi_fasta_sample = SequenceName + '_GenesExtracted.fasta'
+
+  for record in SeqIO.parse(multi_fasta_sample, 'fasta'):
+    individual_file = 'temp_{}_only.fasta'.format(record.id)
+    try:
+      with open(individual_file, 'w') as file:
+        file.write('>' + str(record.id) + '\n' + str(record.seq))
+    except IOError:
+      print(('Error: Could not open file {}'.format(individual_file)))
+      raise
+    except ValueError:
+      print(('Error: File {} is not in the expected format'.format(individual_file)))
+      raise
+
+  # Extract the reference sequences to individual fastas for VIRULIGN processing
+  multi_fasta_ref = SequenceName + '_Reference_GenesExtracted.fasta'
+
+  for record in SeqIO.parse(multi_fasta_ref, 'fasta'):
+    individual_file = 'temp_{}_Reference_only.fasta'.format(record.id)
+    try:
+      with open(individual_file, 'w') as file:
+        file.write('>' + str(record.id) + '\n' + str(record.seq))
+    except IOError:
+      print(('Error: Could not open file {}'.format(individual_file)))
+      raise
+    except ValueError:
+      print(('Error: File {} is not in the expected format'.format(individual_file)))
+
+  # Return error if the [Sample]_GenesExtracted.fasta file is empty
+  if os.path.getsize(multi_fasta_sample) == 0:
+    print(('{} is empty. This can happen if all genes being analysed have missing coverage (? characters). Check MissingCoverage.txt. Now quitting.'.format(multi_fasta_sample)))
+    exit(1)
+  
+  return 0
+
+# Call ExtractRefandSample
+if function_name == 'ExtractRefandSample':
+  ExtractRefandSample(args.AlignmentToRef, args.SingleSeq, args.ReferenceName, args.GeneCoordInfo, args.Gene)
+
+# ExtractSequence takes the specified sequence out of the specified file
+def ExtractSequence(OutputFile, InputFile, SequenceNumber):
+  try:
+    with open(OutputFile, 'w') as file:
+      InputFasta=AlignIO.read(InputFile, 'fasta')
+      Sequence=InputFasta[int(SequenceNumber) - 1]
+      SeqIO.write(Sequence, file, 'fasta')
+  except IOError:
+    print(('Error: Could not open file {}'.format(InputFile)))
+    raise
+  except ValueError:
+    print(('Error: File {} is not in the expected format'.format(InputFile)))
+    raise
+  return 0
+
+# Call ExtractSequence
+if function_name == 'ExtractSequence':
+  ExtractSequence(args.OutputFile, args.InputFile, args.SequenceNumber)
+
+
+# CategoriseIndels classfiies indels as either insertions or deletions based on gaps in the reference
+#  This is slightly biased towards insertions as it will classify an indel as insertion in corrected regions that are not present in the reference (hence gapped)
+def CategoriseIndels(InputFile, OutputCSV, Gene, SequenceName, ReferenceName, GeneCoordInfo, GenomeFile, AlignmentFile, ExtractedGeneFile):
+  SampleNs = []
+  indels = {}
+  try:
+    # Find pre-existing N bases in the sample gene
+    with open(ExtractedGeneFile, 'r') as file:
+      ExtractedGene = SeqIO.read(file, 'fasta')
+      ExtractedSeq = ExtractedGene.seq
+      if 'N' in ExtractedSeq or 'n' in ExtractedSeq:
+        sequence_pos = 0
+        for i, base in enumerate(ExtractedSeq):
+          if base != '-':
+            sequence_pos += 1
+          if base == 'N' or base == 'n':
+            SampleNs.append(int(sequence_pos))
+  except IOError:
+    print(('Error: Could not open file {}'.format(ExtractedGeneFile)))
+    raise
+  except ValueError:
+    print(('Error: File {} is not in the expected format'.format(ExtractedGeneFile)))
+    raise
+      
+  try:
+    # Determine indel type and position
+    with open(InputFile, 'r') as file:
+      sequences = list(SeqIO.parse(file, 'fasta'))
+      reference = sequences[0].seq
+      corrected = sequences[1].seq
+      IndelCount = 0
+      NCount = 0
+      IndelModifier = 0
+      sample_pos = 0
+      gap_count = 0
+      for i, base in enumerate(corrected):
+        if base != '-':
+          sample_pos += 1
+        else:
+          gap_count += 1
+        if base == 'N':
+          if sample_pos in SampleNs: # TODO set this up so if sampleNs is empty it won't compare (ie most sequences)
+            continue
+          else:
+            # Count added N bases in order to determine indel position relative to the original gene
+            NCount += 1
+            # Increase downstream SampleNs by 1 to account for added bases relative to the original gene extraction
+            SampleNs = [x + 1 if x > sample_pos else x for x in SampleNs]
+            # Check if the prior base is not a VIRULIGN-added N - in which case it is included in the prior indel (so only the first base of each indel is used)
+            priorbase = sample_pos - 1
+            if corrected[i - 1] != 'N' or priorbase in SampleNs:
+              if reference[i] == '-':
+                # Modifier to give the position of the actual indel as opposed to the position of the virulign-added Ns. Uses position in the codon
+                # to determine how virulign has corrected the frameshift - i.e. if the N correction is before or after the frameshifting base
+                if (i - gap_count) % 3 == 0:
+                  IndelModifier = 0 # (first base of the codon is N so indel pos needs no adjustment - eg NNB/NBB)
+                elif (i - gap_count) % 3 == 1:
+                  IndelModifier = 1 # (position 1 is an inserted base so indel pos needs to be adjusted by 1 - eg BNN/BNB)
+                else:
+                  if (i - 2) == 'N' and (sample_pos -2) not in SampleNs:
+                    continue # (if NBN then the third N should not be classified as a separate indel)
+                  else:
+                    IndelModifier = 2 # (first two bases are inserted so indel pos needs to be adjusted by 2 - i.e. BBN)
+                # Position of current indel with previous Ns subtracted and -1 to record insertion eith respect to last 'real' base
+                indel_pos = int(sample_pos) - (int(NCount) - 1) - 1 - IndelModifier
+                indels["Indel{}".format(i)] = {"Type": "Insertion", "GenePosition": indel_pos, "Gene": Gene, "Sequence": SequenceName} # Note that IndelN is i value not base position
+                IndelCount += 1
+              else:
+                # Position of current indel with previous Ns subtracted and -1 to record deletion with respect to last 'real' base
+                indel_pos = int(sample_pos) - (int(NCount) -1) - 1
+                indels["Indel{}".format(i)] = {"Type": "Deletion", "GenePosition": indel_pos, "Gene": Gene, "Sequence": SequenceName}
+                IndelCount += 1
+              # Determine indel position relative to the full genome
+              try: 
+                with open('temp_GeneStarts.csv', 'r') as csvfile:
+                  reader = csv.DictReader(csvfile)
+                  for row in reader:
+                    if row['Sequence'] == SequenceName and row['Gene'] == Gene:
+                      gene_start_pos = int(row['GeneStart'])
+                      genome_indel_pos = int(gene_start_pos) - 1 + int(indel_pos)
+                  indels["Indel{}".format(i)].update({"GenomePosition": genome_indel_pos})
+              except IOError:
+                print(('Error: Could not open file {}'.format('temp_GeneStarts.csv')))
+                raise
+              except ValueError:
+                print(('Error: File {} is not in the expected format'.format('temp_GeneStarts.csv')))
+                raise  
+              # Determine indel position relative to the full reference sample alignment - based on the last 'real' ref base so where gaps occur in the ref the position may be imprecise
+              CorrectedAlignment = AlignIO.read(InputFile, 'fasta')
+              ref_indel_pos = len(ungap(CorrectedAlignment[0].seq[0:i])) # For the gene only, not genome
+              ref_gene_start_pos = None
+              try:
+                with open(GeneCoordInfo, 'r') as file:
+                  for line in file:
+                    gene_info = line.strip().split(',')
+                    if gene_info[0] == ReferenceName:
+                      # Assign reference gene starts
+                      if Gene == "GAG":
+                        ref_gene_start_pos = gene_info[1]
+                      elif Gene == "POL":
+                        ref_gene_start_pos = gene_info[3]
+                      elif Gene == "VIF":
+                        ref_gene_start_pos = gene_info[5]
+                      elif Gene == "VPR":
+                        ref_gene_start_pos = gene_info[7]
+                      elif Gene == "VPU":
+                        ref_gene_start_pos = gene_info[9]
+                      elif Gene == "ENV":
+                        ref_gene_start_pos = gene_info[11]
+                      elif Gene == "NEF":
+                        ref_gene_start_pos = gene_info[13]
+                      else:
+                        print('Could not match gene name to any of the expected inputs. Quitting')
+                        exit(1)
+                      break
+                    else:
+                      continue
+                  if ref_gene_start_pos is None:
+                    print('Could not match the reference sequence to any within the reference file. Quitting.')
+                    exit(1)
+              except IOError:
+                print(('Error: Could not open file {}'.format(GeneCoordInfo)))
+                raise
+              except ValueError:
+                print(('Error: File {} is not in the expected format'.format(GeneCoordInfo)))
+                raise
+              if ref_gene_start_pos is not None:
+                ref_genome_indel_pos = int(ref_gene_start_pos) - 1 + int(ref_indel_pos) # Not included in Frameshifts.csv
+                try: 
+                  with open(GenomeFile, 'r') as file:
+                    genome_records = SeqIO.to_dict(SeqIO.parse(file, "fasta"))
+                    for record_id, record in list(genome_records.items()):
+                      if record_id == ReferenceName:
+                        GlobalSeq = record.seq
+                        sequence_pos = 0
+                        for j in range(len(GlobalSeq)):
+                          if GlobalSeq[j] != '-':
+                            sequence_pos += 1
+                          if sequence_pos == ref_genome_indel_pos:
+                            global_ref_indel_pos = int(j) + 1
+                            indels["Indel{}".format(i)].update({"GlobalGenomeRefPosition": global_ref_indel_pos})
+                            break
+
+                except IOError:
+                  print(('Error: Could not open file {}'.format(GenomeFile)))
+                  raise
+                except ValueError:
+                  print(('Error: File {} is not in the expected format'.format(GenomeFile)))
+                  raise
+      
+              else:
+                print(('Unable to find the reference gene start for {}. Quitting.'.format(Gene)))
+              
+              # Determine position relative to HXB2
+              try:
+                with open(AlignmentFile, 'r') as file:
+                  HXB2Alignment = AlignIO.read(file, 'fasta')
+                  sequence_pos = 0
+                  for j in range(len(HXB2Alignment[0].seq)):
+                    if HXB2Alignment[0][j] != '-':
+                      sequence_pos += 1
+                    if sequence_pos == genome_indel_pos:
+                      hxb2_alignment_pos = j
+                      hxb2_indel_pos = len(ungap(HXB2Alignment[1].seq[0:int(hxb2_alignment_pos) + 1]))
+                      indels["Indel{}".format(i)].update({"HXB2Position": hxb2_indel_pos})
+                      break
+              except IOError:
+                print(('Error: Could not open file {}'.format(AlignmentFile)))
+                raise
+              except ValueError:
+                print(('Error: File {} is not in the expected format'.format(AlignmentFile)))
+                raise
+              
+      # Write indels to CSV
+      with open(OutputCSV, 'a', newline='') as csvfile:
+        fieldnames = ['Sequence', 'Gene', 'IndelID', 'Type', 'GenePosition', 'GenomePosition', 'GlobalGenomeRefPosition', 'HXB2Position']
+        writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
+        if csvfile.tell() == 0:
+          writer.writeheader()
+        for indel_id, data in list(indels.items()):
+          writer.writerow({'Sequence': data['Sequence'], 'Gene': data['Gene'], 'IndelID': indel_id, 'Type': data['Type'], 'GenePosition': data['GenePosition'], 'GenomePosition': data['GenomePosition'], 'GlobalGenomeRefPosition': data['GlobalGenomeRefPosition'], 'HXB2Position': data['HXB2Position']})
+
+  except IOError:
+    print(('Error: Could not open file {}'.format(InputFile)))
+    raise
+  except ValueError:
+    print(('Error: File {} is not in the expected format'.format(InputFile)))
+    raise
+  return 0
+
+# Call CategoriseIndels
+if function_name == 'CategoriseIndels':
+  CategoriseIndels(args.InputFile, args.OutputCSV, args.Gene, args.SequenceName, args.ReferenceName, args.GeneCoordInfo, args.GenomeFile, args.AlignmentFile, args.ExtractedGeneFile)
diff --git a/bin/tools/CodonCorrection.sh b/bin/tools/CodonCorrection.sh
new file mode 100755
index 0000000..92193cc
--- /dev/null
+++ b/bin/tools/CodonCorrection.sh
@@ -0,0 +1,713 @@
+#!/usr/bin/env bash
+
+# CodonCorrection.sh is a script designed to call the program 'VIRULIGN' which pairwise aligns viral sequences in a codon-correct manner. Using a set of provided
+# references known to be codon-correct and a list of their gene coordinates (see the CodonCorrectionInit.sh), the script will extract the selected genes from the 
+# sample and the reference determined to be the closest BLAST match. This is done per individual gene, meaning the reference can be different for each. Each gene
+# and the corresponding reference is then fed into VIRULIGN, which will correct the gene sequence by adding 'N' bases to preserve the reading frame in the event of 
+# insertions or deletions relative to the reference. The results of this can be viewed in the [Nucl/AminoAcids/Mutations/Mutations]_corrected files depending on 
+# the options chosen. If the 'Mutations' option is used, a text file listing frameshifts will be produced for subsequent analysis. 
+
+# CodonCorrectionInit.sh must be run once before running this script
+
+# Explanation of the virulign export options:
+# Within this script, there are four different options for the format of the virulign output, which are set in the third argument of the CodonCorrection.sh command.
+# Multiple output formats can be generated simultaneously when separated by ',', or use 'all' to generate all four. Each output file will be generated per chosen gene.
+  # 1. Nucleotides: will generate a FASTA file of the target nucleotide sequences, with the sample sequence aligned to the reference sequence. This is set to always
+  #    be generated as it allows CodonCorrection.sh to check that the sample sequence has not been truncated by VIRULIGN (an issue I observed with some sequences - in 
+  #    this event the reference sequence is artificially extended using 'N'.).
+  # 2. AminoAcids: will generate a FASTA file of the target amino acid sequences, with the sample sequence aligned to the reference sequence. 
+  # 3. Mutations: will output for each gene a list of amino acids changes compared to the reference sequence. This must be enabled in order to generate the file listing
+  #    frameshifts.
+  # 4. MutationTable: will create a CSV file where each mutation present at a specific position is given as a separate column in Boolean representation. The CSV file is 
+  #    annotated according to the numerical position in the protein
+
+# Currently only handles the uninterrupted genes GAG POL VIF VPR VPU ENV and NEF.
+
+set -u
+set -o pipefail
+set -e
+
+UsageInstructions="Arguments for this script:
+(1) A sample file containing the sequence to be corrected as the first sequence;
+(2) The filepath for the virulign binaries
+(3) The export options for virulign separated by ',' and enclosed by double quotes. One of more of Mutations, MutationTable, Nucleotides, or Amino Acids, \
+or use 'all' to generate all four.
+(4) The chosen genes to analyse for the sample separated by ',' and enclosed by double quotes. One or more of gag, pol, env, vpr, vif, vpu, or nef, \
+or use 'all' to analyse all.
+(5) The init directory.
+(6) The directory where output files will be created.
+(7) OPTIONAL - The number corresponding to how close the BLAST match should be for this run. E.g. the top match is 1, second highest is 2, etc. Default is 1.
+"
+
+# Check arguments
+ExpectedArgs=6
+OptionalArgs=7
+if [[ $# -ne "$ExpectedArgs" ]] && [[ "$#" -ne "$OptionalArgs" ]]; then
+  echo "$UsageInstructions"
+  echo "Incorrect number of arguments provided, expected:" "$ExpectedArgs" "or" "$OptionalArgs" "arguments if selecting which BLAST match number to use." "Quitting." >&2
+  exit 1
+else
+  SampleFile=$1
+  VirulignLocation=$2
+  VirulignOptions=$3
+  GenesToAnalyse=$4
+  InitDir=$5
+  OutputDir=$6
+  if [[ $# -eq 6 ]]; then
+    BLASTMatch=1
+  elif [[ $# -eq 7 ]]; then
+    BLASTMatch=$7
+  fi
+fi
+
+# Find shiver files
+ToolsDir="$(cd "$(dirname "${BASH_SOURCE[0]}" )" && pwd)"
+shiver="$(cd "$(dirname "${BASH_SOURCE[0]}" )"/../.. && pwd)"
+DataDir="$shiver"/'data'
+shiver_bin="$(dirname "$ToolsDir")"
+source "$shiver_bin"/'config.sh'
+PythonFuncs="$shiver_bin"/'tools/CC_Python_funcs.py'
+ReferenceFile="$InitDir/CC_References.fasta"
+GeneCoordInfo="$InitDir/CC_Coords.fasta"
+HXB2File="$DataDir"/'external/B.FR.83.HXB2_LAI_IIIB_BRU.K03455.fasta'
+AlignMoreSeqsTool="$shiver_bin"/'tools/AlignMoreSeqsToPairWithMissingCoverage.py'
+
+# Colours # NB Make things more readable in the terminal but can be removed e.g. for cluster usage - a variable is set in the config file to disable them
+if [[ "$CC_EnableColours" == "true" ]]; then
+  RED="\033[91m"
+  BLUE="\033[94m"
+  YELLOW="\033[93m"
+  GREEN="\033[92m"
+  GREY="\033[37m"
+  END="\033[0m"
+else
+  RED=""
+  BLUE=""
+  YELLOW=""
+  GREEN=""
+  GREY=""
+  END=""
+fi
+
+# Check init script has been run # NB this is being triggered with my attempt into calling within shiver, so there is a mismatch in the files somewhere (init file has wrong path,
+#   or this script has wrong init path)
+if [[ ! -s "$ReferenceFile" ]] || [[ ! -s "$GeneCoordInfo" ]]; then
+  echo "Reference file and/or the coordinates file are not found in the init directory. Please run CodonCorrectionInit.sh before running this script. Quitting." >&2
+  exit 1
+fi
+
+# Check if file exists
+if ! [[ -f "$SampleFile" ]]; then
+  echo "The provided sample file '$SampleFile' does not exist. Check the file path is correct."
+  exit 1
+fi
+
+# Check sample is a .fasta file
+if [[ "$SampleFile" != *.fasta ]]; then 
+  echo "Sample file $SampleFile is not a fasta file. Quitting." >&2
+  exit 1
+fi
+
+# Count sequence number in sample 
+Sample_SeqNumber=$(grep '^>' "$SampleFile" | wc -l | awk '{$1=$1};1')
+if [[ "$Sample_SeqNumber" == 0 ]]; then
+  echo "Reference file $ReferenceFile contains no sequences. Quitting." >&2
+  exit 1
+fi
+
+# Check HXB2 file exists within shiver
+if ! [[ -f "$HXB2File" ]]; then
+  echo "Unable to find the HXB2 file within shiver: $HXB2File. Quitting." >&2
+  exit 1
+fi
+
+# Determine whether to use mafft pairwise or AlignMoreSeqs
+if [[ "$Sample_SeqNumber" == 1 ]]; then
+  SingleSequence=true # Will be funneled into mafft pairwise alignment
+elif [[ "$Sample_SeqNumber" == 2 ]]; then
+  SingleSequence=false # In this case CC.sh expects remap consensus files (=2 sequences) and will use the AlignMoreSeqs tool which can handle missing coverage.
+else 
+  echo "Unexpected number of sequences in the sample file. Expected 1 or 2. Quitting." >&2
+  exit 1
+fi
+
+# Check VIRULIGN exists
+if [[ ! -f "$VirulignLocation" ]]; then
+  echo "The specified VIRULIGN location '$VirulignLocation' does not exist. Check file path is correct. Quitting." >&2
+  exit 1
+fi
+
+# Check VIRULIGN
+"$VirulignLocation" &> /dev/null || echo "Error running VIRULIGN. Check the program is installed correctly." >&2
+
+# cd to $OutputDir
+if [[ -d "$OutputDir" ]]; then
+  echo "$OutputDir exists already; quitting to prevent overwriting." >&2
+  exit 1
+fi
+mkdir -p "$OutputDir" && cd "$OutputDir" ||
+{ echo "Unable to change directory to $OutputDir. Quitting." >&2 ; exit 1 ; }
+
+# Determine VIRULIGN options
+Nucleotides=false
+AminoAcids=false
+Mutations=false
+MutationTable=false
+
+VirulignOptionsHelp="CodonCorrection.sh can run VIRULIGN with four distinct output formats. To specify \
+which, pass up to four of the following options to CodonCorrection.sh enclosed by double quotes and separated by commas.
+See the VIRULIGN tutorial for more information on these options.
+(1) Nucleotides: An aligned sequence of corrected nucleotides.
+(2) AminoAcids: An aligned sequence of corrected amino acids.
+(3) Mutations: A list of amino acids changes compared to the reference sequence, including frameshifts.
+(4) MutationTable: A CSV file where each mutation present at a specific position is given as a separate column in Boolean representation.
+"
+
+# Select VIRULIGN options
+VirulignOutput=("Nucleotides" "AminoAcids" "Mutations" "MutationTable")
+if [[ "$VirulignOptions" == "all" ]]; then 
+  Nucleotides=true
+  AminoAcids=true
+  Mutations=true
+  MutationTable=true
+else
+  # Select alignment output based on VirulignOptions args
+  IFS=',' read -ra listed_options <<< "$VirulignOptions"
+  for option in "${listed_options[@]}"; do
+    # Could convert to all upper/lowercase here (and change variable names) for consistency
+    if [[ " ${VirulignOutput[*]} " == *" $option "* ]]; then
+      eval "${option}=true"
+    else
+      echo "Error: '$option' is not a valid option. Valid options are Nucleotides, AminoAcids, Mutations, MutationTable. Quitting."
+      echo "$VirulignOptionsHelp"
+      exit 1
+    fi
+  done
+fi
+
+### Determine which genes to correct
+GAG=false
+POL=false
+VIF=false
+VPR=false
+VPU=false
+ENV=false
+NEF=false
+
+genes=("GAG" "POL" "VIF" "VPR" "VPU" "ENV" "NEF") # NB this is now defined in the config but I forgot to remove here - out of time to test so won't remove just in case!  
+
+# Switch on all genes if command set to "all"
+if [[ "$GenesToAnalyse" == "all" ]]; then
+  GAG=true
+  POL=true
+  VIF=true
+  VPR=true
+  VPU=true
+  ENV=true
+  NEF=true
+else
+  # Switch on the corresponding gene variable for each listed gene
+  IFS=',' read -ra listed_genes <<< "$GenesToAnalyse"
+  for gene_name in "${listed_genes[@]}"; do
+      # Convert gene name to uppercase
+      gene_upper=$(echo "$gene_name" | tr '[:lower:]' '[:upper:]')
+
+      # Check if the gene name is valid
+      if [[ " ${genes[*]} " == *" $gene_upper "* ]]; then
+        eval "${gene_upper}=true"
+      else
+        echo "Error: '$gene_name' is not a valid gene name. Valid gene names are: GAG, POL, ENV, VPR, VIF, VPU, NEF." >&2
+        exit 1
+      fi
+  done
+fi
+
+# Extracting the sample ID from the sample fasta file
+SequenceName_shell=$(head -n 1 "$SampleFile" | sed 's/>//')
+
+###################################################################################
+
+# Print chosen genes
+listed_genes=()
+for gene in "${genes[@]}"; do
+  if [[ "${!gene}" = true ]]; then
+    listed_genes+=(" $gene")
+  fi
+done
+
+if [[ "${#listed_genes[@]}" -gt 0 ]]; then
+  echo -e "${BLUE}Outputting files for chosen options: ${listed_genes[@]} ${END}"
+else
+  echo "No genes selected for codon correction. Quitting."
+  exit 1
+fi
+
+# Function to align the sample to the chosen reference
+  # Both mafft options are set to quiet to avoid obfuscating error messages, but this can be switched off by removing the '---quiet' options below
+function align_to_sample {
+  AlignmentRef="$1"
+  AlignmentAppend="$2"
+
+  if [[ "$AlignmentRef" == "$HXB2File" ]]; then
+    OutputAlignment=temp_"$SequenceName_shell$AlignmentAppend"
+  else
+    OutputAlignment="$SequenceName_shell$AlignmentAppend"
+  fi
+
+  if [[ "$SingleSequence" == 'true' ]]; then
+    # Carry out a mafft pairwise alignment - this assumes that single sequences do not contains the '?' characters found within shiver output files 
+    "$mafft" --quiet --add "$AlignmentRef" "$SampleFile" > "$OutputAlignment"
+  else
+    # Capable of handling sequence with unknown coverage in parts. Requires two sequences in the starting sample .fasta
+    "$python" "$AlignMoreSeqsTool" --x-mafft "$mafft --quiet" "$AlignmentRef" "$SampleFile" > "$OutputAlignment"
+  fi
+
+}
+
+# Align sample to HXB2 in preparation for gene extraction
+align_to_sample "$HXB2File" "_HXB2Aligned.fasta" || { echo "Problem aligning sample with reference HXB2. Quitting." >&2; exit 1; }
+HXB2_Alignment=temp_"$SequenceName_shell$AlignmentAppend"
+
+# Extract approximate sample genes using HXB2 as a reference - only used to BLAST to reference genes before more precise sample extraction
+"$python" "$PythonFuncs" ExtractWithHXB2 --AlignmentFile "$HXB2_Alignment" --SingleSeq "$SingleSequence" || { echo "CodonCorrection.sh was unable to extract the sample gene sequences. Quitting." >&2; exit 1; }
+
+# Check if genes have entered MissingCoverage.txt, and if so omit from further processing
+if [[ -s "MissingCoverage.txt" ]]; then
+  for gene in "${genes[@]}"; do
+    if [[ "${!gene}" = true ]]; then
+      if grep -q "$SequenceName_shell"_"${gene}" "MissingCoverage.txt"; then
+          eval "$gene=false"
+      fi
+    fi
+  done
+fi
+
+# BLASTn the sample sequences to the corresponding gene database
+function blastn_to_genes() {
+  MaxTargets="$BLASTMatch" # Ensures that enough targets are listed - could be set to a static value instead of an arg, or a minimum of N.
+  for gene in "${genes[@]}"; do
+    if [[ "${!gene}" = true ]]; then
+      BLASTn_Database="$InitDir/BLASTnDB_${gene}"
+      BLAST_Gene=/"$OutputDir"/temp_preBLAST_Sample_Gene_"${gene}".fasta
+      BLAST_Output=blastn_"${gene}".out
+      # Run BLASTn
+      "$BlastNcommand" -query "$BLAST_Gene" -db "$BLASTn_Database"/"${gene}" -outfmt \
+      "10 qseqid qseq evalue sseqid pident qlen qstart qend sstart send bitscore" -out "$BLAST_Output" -max_target_seqs "$MaxTargets" \
+      || { echo "Failed to execute BLASTn command. Quitting." >&2; return 1; }
+      
+      # Assign the nth closest reference name per gene, where n is the specified nth closest match (1 is 1st, 2 is 2nd, etc.)
+      ExtractMatch="$(awk -F',' '{print $11, $0}' "$BLAST_Output" | sort -rn | awk -F',' -v rank="$BLASTMatch" 'NR==rank {print $4}' | sed 's/^[[:space:]]*//')"
+      ExtractSeqName=${ExtractMatch%????}
+
+      # Assign a reference variable for each gene
+      GeneRef="ref_$gene"
+      eval "$GeneRef=$ExtractSeqName"
+      # List reference to shell
+      echo -e "${GREEN}Reference used for ${gene}: ${!GeneRef}${END}"
+    fi
+  done
+  return 0
+}
+
+# Call BLASTn function
+blastn_to_genes || { echo "Problem BLASTing sample genes to the corresponding gene database. Quitting." >&2; exit 1; }
+
+# Extract the reference sequence from the full references list for each gene
+for gene in "${genes[@]}"; do
+  if [[ "${!gene}" = true ]]; then
+    GeneRef="ref_$gene"
+    "$python" "$PythonFuncs" ExtractRefFromFasta --ReferenceName "${!GeneRef}" --GenomeFile "$ReferenceFile" --Gene "$gene" || { echo "CodonCorrection.sh was unable to extract the reference sequence from the list of references. Quitting." >&2; exit 1; }
+  fi
+done
+
+# Assign the reference genome as a variable for each gene
+for gene in "${genes[@]}"; do
+  if [[ "${!gene}" = true ]]; then
+    ReferenceGenome="ref_genome_$gene"
+    eval "$ReferenceGenome=temp_Reference_Genome_$gene.fasta"
+  fi
+done
+
+# Align the sample genome to the reference genome for each gene and extract the sample and reference genes
+  # Sample genes have been extracted with HXB2 already (although perhaps less accurately as it just uses HXB2 to align and extract) 
+  # and the reference genes were extracted as part of the init. Because this script is already written I'm keeping it for the updated 
+  # gene-by-gene processing, but it could be modified/removed due to those preexisting files.
+for gene in "${genes[@]}"; do
+  if [[ "${!gene}" = true ]]; then
+    ReferenceGenome="ref_genome_$gene"
+    GeneRef="ref_$gene"
+    align_to_sample "${!ReferenceGenome}" "_AlignedSeqs_$gene.fasta" || { echo "Problem aligning sample with reference genome. Quitting." >&2; exit 1; }
+    # Assign the reference alignment file
+    ReferenceAlignment="$SequenceName_shell"_AlignedSeqs_$gene.fasta # This variable will only work within the loop
+
+   # Run python script to extract the final sample and reference genes
+     # Names of output files could be confusing? Rename if needed
+   "$python" "$PythonFuncs" ExtractRefandSample --AlignmentToRef "$ReferenceAlignment" --SingleSeq "$SingleSequence" --ReferenceName "${!GeneRef}" --GeneCoordInfo "$GeneCoordInfo" --Gene "${gene}" || { echo "CodonCorrection.sh was unable to extract the genes for reference and sample. Quitting." >&2; exit 1; }
+  fi
+done
+
+###################################################################################
+
+# Print chosen virulign options
+listed_options=()
+for option in "${VirulignOutput[@]}"; do
+  if [[ "${!option}" = true ]]; then
+    listed_options+=(" $option")
+  fi
+done
+if [[ "${#listed_options[@]}" -gt 0 ]]; then
+  echo -e "${BLUE}Outputting files for chosen options: ${listed_options[@]} ${END}"
+else
+  echo -e "${RED}Problem with chosen virulign options. Quitting.${END}" >&2
+  exit 1
+fi
+
+# Override for Nucleotides - in order to correctly analyse length this is always set to true # NB should be incorporated into when virulign options are initially set
+Nucleotides=true
+
+# Initialise variables
+export_alphabet=""
+export_kind=""
+FileAppend=""
+ErrorFile="FailedAlignment.txt"
+
+# Define a function to call virulign
+function run_virulign {
+  export_alphabet_func="$1"
+  export_kind_func="$2"
+  FileAppend_func="$3"
+  # Setting a max value for frameshifts arbitrarily due to frameshift errors occuring in highly variable genes - although in the gene I tested the same "Frameshift Error"
+  # occured within VIRULIGN regardless of this value.
+  MaxFrameshifts=20
+  GapExtensionPenalty=3.3 # default virulign is 3.3
+  GapOpenPenalty=10.0 # default virulign is 10.0
+
+  # Find sample and reference files
+  for gene in "${genes[@]}"; do
+    if [[ "${!gene}" == true ]]; then
+      GeneRef="ref_$gene"
+      SampleGene=$(find . -type f -name "temp_${SequenceName_shell}_${gene}_only.fasta")
+      ReferenceGene=$(find . -type f -name "temp_${!GeneRef}_${gene}_Reference_only.fasta")
+
+      if [[ -n "$SampleGene" ]]; then
+        # Run VIRULIGN
+        v_output=$( { $VirulignLocation $ReferenceGene $SampleGene --exportKind $export_kind_func --exportAlphabet $export_alphabet_func --exportReferenceSequence yes \
+          --exportWithInsertions yes --gapExtensionPenalty $GapExtensionPenalty --gapOpenPenalty $GapOpenPenalty --maxFrameShifts $MaxFrameshifts; } 2>&1 > HIV_${gene}$FileAppend_func )
+        echo -e "${GREY}$v_output${END}"
+
+        # Check for errors
+        touch "$ErrorFile"
+        if echo "$v_output" | grep -qi 'error'; then
+          error_line=$(echo "$v_output" | grep -i 'error')
+          if ! grep -qF "$error_line" "$ErrorFile"; then
+            echo "$error_line" >> "$ErrorFile"
+          fi
+        fi
+      else
+        echo "Skipping virulign analysis of ${gene} due to missing coverage."
+      fi
+    fi
+  done
+}
+
+# Function to call the run_virulign function with the chosen VIRULIGN options
+function call_virulign {
+  # Define virulign command options based on chosen output options
+  for option in "${VirulignOutput[@]}"; do
+    if [[ "${!option}" == "true" ]]; then
+      # Set variables for each virulign output option
+      case "$option" in
+        "Nucleotides")
+          export_alphabet="Nucleotides"
+          export_kind="GlobalAlignment"
+          FileAppend="_Nucl_corrected.fasta"
+          ;;
+        "AminoAcids")
+          export_alphabet="AminoAcids"
+          export_kind="GlobalAlignment"
+          FileAppend="_AminoAcids_corrected.fasta"
+          ;;
+        "Mutations")
+          export_alphabet="Nucleotides"
+          export_kind="Mutations"
+          FileAppend="_Mutations.csv"
+          ;;
+        "MutationTable")
+          export_alphabet="AminoAcids"
+          export_kind="MutationTable"
+          FileAppend="_MutationTable.csv"
+          ;;
+      esac
+  
+      if [[ -z $export_alphabet || -z $export_kind || -z $FileAppend ]]; then
+          echo -e "${RED}Error: One or more options are not set. Quitting.${END}"
+          exit 1
+      fi
+
+     # Run virulign
+     run_virulign "$export_alphabet" "$export_kind" "$FileAppend" || { echo "Problem running virulign. Quitting." >&2; exit 1; }
+
+    fi
+  done
+}
+
+# Call virulign with chosen options
+call_virulign || { echo "Problem calling virulign with the selected options. Quitting." >&2; exit 1; }
+
+
+# Check for single sequences in output (indicates failed as they should be paired)
+for gene in "${genes[@]}"; do
+  # Check Nucleotides aligned successfully
+  if [[ "$Nucleotides" == "true" ]]; then
+    if [[ -f  "HIV_${gene}_Nucl_corrected.fasta" ]]; then
+      sequence_num_nucl=$(grep ">" "HIV_${gene}_Nucl_corrected.fasta" | wc -l)
+      if [[ "$sequence_num_nucl" -lt 2 ]]; then
+        # Set gene value to false so it's not used for subsequent analysis
+        eval "$gene=false"
+        echo -e "${YELLOW}Due to failed nucleotide alignment ${gene} will be omitted from further processing.${END}"
+        # If not already in the failed alignments error file, then note the error
+        if ! grep -qE "^${SequenceName_shell}_${gene}" "$ErrorFile"; then
+          echo "${SequenceName_shell}_${gene} failed to produce an alignment." >> "$ErrorFile"
+        fi
+        continue
+      fi
+    fi
+  fi
+  # Check amino acids aligned successfully
+  if [[ "$AminoAcids" == "true" ]]; then
+    if [[ -f  "HIV_${gene}_AminoAcids_corrected.fasta" ]]; then
+      sequence_num_AA=$(grep ">" "HIV_${gene}_AminoAcids_corrected.fasta" | wc -l)
+      if [[ "$sequence_num_AA" -lt 2 ]]; then
+        # Set gene value to false so it's not used for subsequent analysis
+        eval "$gene=false"
+        echo -e "${YELLOW}Due to failed amino acid alignment ${gene} will be omitted from further processing.${END}"
+        # If not already in the failed alignments error file, then note the error
+        if ! grep -qE "^${SequenceName_shell}_${gene}" "$ErrorFile"; then
+          echo "${SequenceName_shell}_${gene} failed to produce an alignment." >> "$ErrorFile"
+        fi
+        continue
+      fi
+    fi
+  fi
+  # Check Mutations file analysed both sequences 
+  if [[ "$Mutations" == "true" ]]; then
+    # Extract frameshift information
+    if [[ -f "HIV_${gene}_Mutations.csv" ]]; then
+      MutationCheck=$(awk -F ',' 'NR==3 {print $2}' "HIV_${gene}_Mutations.csv")
+      # Check if the alignment failed
+      if [[ "$MutationCheck" == "Failure" ]]; then
+        # Set gene value to false so it's not used for subsequent analysis
+        eval "$gene=false"
+        echo -e "${YELLOW}Due to failed nucleotide alignment ${gene} will be omitted from further processing.${END}"
+        # If not already in the failed alignments error file, then note the error
+        if ! grep -qE "^${SequenceName_shell}_${gene}" "$ErrorFile"; then
+          echo "${SequenceName_shell}_${gene} failed to produce an alignment." >> "$ErrorFile"
+        fi
+        continue
+      fi
+    fi
+  fi
+  # Check Mutation table contains both sequences
+  if [[ "$MutationTable" == "true" ]]; then
+    # Count lines
+    if [[ -f "HIV_${gene}_MutationTable.csv" ]]; then
+      mt_line_count=$(cat "HIV_${gene}_MutationTable.csv" | wc -l)
+      if [[ "$mt_line_count" -eq 2 ]]; then
+        # Set gene value to false so it's not used for subsequent analysis
+        eval "$gene=false"
+        echo -e "${YELLOW}Due to failed amino acid alignment ${gene} will be omitted from further processing.${END}"
+        # If not already in the failed alignments error file, then note the error
+        if ! grep -qE "^${SequenceName_shell}_${gene}" "$ErrorFile"; then
+          echo "${SequenceName_shell}_${gene} failed to produce an alignment." >> "$ErrorFile"
+        fi
+        continue  
+      fi
+    fi
+  fi
+done
+
+# Function to add length to the reference
+  # Adds codon-correct number of N's to the temp reference file. For some samples if the reference is shorter than the sample sequence, VIRULIGN will prematurely 
+  # truncate the sequence to be the same length as the reference. This can be negated by adding generic 'N' bases to the reference. Ideally VIRULIGN would 
+  # be adjusted to not require this (I'm unable to find anything within the present options) - but I don't have the C++ knowledge to correct this.
+function add_length {
+  LengthChange=$1
+  Gene=$2
+  ReferenceGene=$(find . -type f -name "temp_${!GeneRef}_${gene}_Reference_only.fasta")
+  NsToAdd=""
+
+  # Extract the sample sequence from the first round of virulign correction
+  "$python" "$PythonFuncs" ExtractSequence --OutputFile "temp_${SequenceName_shell}_${Gene}_Corrected.fasta" --InputFile "HIV_${Gene}_Nucl_corrected.fasta" --SequenceNumber "2" || { echo "Problem extracting the corrected gene sequence. Quitting." >&2; return 1; }
+  # Determine if any bases are missing from the start of the virulign output by aligning the extracted and corrected gene
+  SampleAlignment="temp_${SequenceName_shell}_${Gene}_SampleAlignment.fasta"
+  "$mafft" --quiet --add "temp_${SequenceName_shell}_${Gene}_only.fasta" "temp_${SequenceName_shell}_${Gene}_Corrected.fasta" > "$SampleAlignment"
+
+  # Count the gaps at the start of the corrected sequence (i.e. the shift in gene positions of the sample sequence)
+  PositionShift=0
+  PositionShift=$(awk 'NR==2 {if(match($0, /^[-]+/)) print RLENGTH; else print 0}' "$SampleAlignment")
+  if [[ "$LengthChange" -lt 0 ]]; then
+    echo -e "${YELLOW}The VIRULIGN-corrected $Gene sequence has a change in length of $LengthChange${END}"
+    echo "${SequenceName_shell}_$Gene had a change in length of $LengthChange before correction.">> "$LengthFile"
+    # Convert to positive number (length change is always negative for truncation issues)
+    LengthChange=$((LengthChange * -1))
+    # Determine change in length at the end of the sequence
+    EndLength=$((LengthChange - PositionShift))
+    if [[ "$EndLength" != 0 ]]; then
+      # Determine length of N string to add
+      if ((EndLength % 3 == 0)); then
+        N_Number=$EndLength
+      elif ((EndLength % 3 == 1)); then
+        N_Number=$((EndLength + 2))
+      elif ((EndLength % 3 == 2)); then
+        N_Number=$((EndLength + 1))
+      fi
+      # Create N string
+      for ((i=0; i<N_Number; i++)); do
+        NsToAdd+="N"
+      done
+      echo "$(cat $ReferenceGene)$NsToAdd" > "$ReferenceGene"
+    fi
+
+    # Add length to the start of the sequence
+    if [[ "$PositionShift" != 0 ]]; then
+      NsToAdd=""
+      for ((i=0; i<PositionShift; i++)); do
+        NsToAdd+="N"
+      done
+      awk 'NR==2 {print "'"$NsToAdd"'" $0; next} 1' "$ReferenceGene" > temp_file && mv temp_file "$ReferenceGene"
+    fi
+
+    # OPTION 1: Delete old results
+    # Delete old virulign results - For testing purposes files are renamed as below, can revert to deletion
+    # rm -f ./HIV_${Gene}_Nucl_corrected.fasta
+    # rm -f ./HIV_${Gene}_AminoAcids_corrected.fasta
+    # rm -f ./HIV_${Gene}_Mutations.csv
+    # rm -f ./HIV_${Gene}_MutationTable.csv
+
+    # OPTION 2: Rename virulign results
+    mv -f ./HIV_${Gene}_Nucl_corrected.fasta ./HIV_${Gene}_Nucl_corrected_OLD.fasta
+    mv -f ./HIV_${Gene}_AminoAcids_corrected.fasta ./HIV_${Gene}_AminoAcids_corrected_OLD.fasta
+    mv -f ./HIV_${Gene}_Mutations.csv ./HIV_${Gene}_Mutations_OLD.csv
+    mv -f ./HIV_${Gene}_MutationTable.csv ./HIV_${Gene}_MutationTable_OLD.csv
+    
+    # Set all other gene variables to false in order to re-run virulign with only the modified gene references
+    local GAG=false
+    local POL=false
+    local VIF=false
+    local VPR=false
+    local VPU=false
+    local ENV=false
+    local NEF=false
+
+    if [[ "${genes[*]}" == *"$Gene"* ]]; then
+      eval "${Gene}=true"
+    fi
+
+    # Call virulign again to analyse using new reference lengths 
+    call_virulign || { echo "Problem calling virulign after length correction. Quitting." >&2; return 1; }
+  fi
+
+}
+
+# Compare sequence length of the extracted sample to final corrected sequence
+if [[ "$Nucleotides" == "true" ]]; then
+  LengthFile="CorrectedLengthSeqs.txt"
+  for gene in "${genes[@]}"; do
+    GeneRef="ref_$gene"
+    if [[ "${!gene}" = true ]]; then
+      SampleGene=$(find . -type f -name "temp_${SequenceName_shell}_${gene}_only.fasta")
+      # Determine lengths - ignore gaps and added Ns to determine only 'real' changes in lengths, ie false truncation/extension
+      if [[ -s "HIV_${gene}_Nucl_corrected.fasta" ]] && [[ -f "$SampleGene" ]]; then
+        extracted_seq_length=$(awk -v gene="${gene}" -v seq_name="${SequenceName_shell}" '/^>/{if ($0 ~ seq_name "_" gene) found=1; else found=0; \
+        next} found { gsub("-", "", $0); len+=length($0) } END{print len}' "$SampleGene") # add error checks to these if failed
+        # Find the number of pre-existing N's in the sample gene
+        ExistingNs=$(tail -n +2 "$SampleGene" | tr -cd 'Nn' | wc -c | awk '{print $1+0}')
+        v_output_sample_seq_length=$(awk -v gene="${gene}" -v seq_name="${SequenceName_shell}" '/^>/{if ($0 ~ seq_name "_" gene) found=1; else found=0; \
+        next} found { gsub("-", "", $0); gsub("N", "", $0); len+=length($0) } END{print len}' "HIV_${gene}_Nucl_corrected.fasta")
+        v_output_sample_seq_length=$((v_output_sample_seq_length + ExistingNs))
+        # Calculate difference in sequence length and add length if needed
+        seq_difference=$((v_output_sample_seq_length - extracted_seq_length))
+        if [[ "$seq_difference" -lt 0 ]]; then
+          add_length "$seq_difference" "${gene}" || { echo "Problem adding length to reference files. Quitting." >&2; exit 1; }
+        fi
+      fi
+    fi
+  done
+fi
+
+# Error message for truncated/extended sequences
+if [[ -s $LengthFile ]]; then
+  echo -e "${YELLOW}Virulign output files for truncated sample sequences have been deleted. Virulign has been run again with the reference sequence extended for those genes. Ignore the added \
+terminal N bases in subsequent analysis - the unmodified reference sequence remains in ${SequenceName_shell}_Reference_GenesExtracted.fasta.
+As a result of this some positional/mutation information for the reference sequence may be incorrect due to artifical bases being added - eg X mutations in the reference.${END}"
+  echo -e "${YELLOW}Check $LengthFile for details of which sequences had their references extended.${END}"
+fi
+
+# Check if any alignments failed
+if [[ -s "$ErrorFile" ]]; then
+  echo -e "${YELLOW}Not all alignments were successful, check $ErrorFile${END}"
+elif [[ -f "$ErrorFile" ]]; then
+  rm "$ErrorFile"
+fi
+
+# Print frameshift info to file
+if [[ ! -f "Frameshifts.txt"  ]] && [[ "$Mutations" == "true" ]]; then
+  echo "Sequence Name, Frameshift quantity, Mutations" > Frameshifts.txt
+fi
+
+if [[ -f "Frameshifts.txt" ]] && [[ "$Mutations" == "true" ]]; then
+  # Extract frameshift information
+  for gene in "${genes[@]}"; do
+    if [[ -f "HIV_${gene}_Mutations.csv" ]]; then
+      frameshift_info=$(awk -F ',' 'NR==3 {print $1 ", " $4 ", " $7}' "HIV_${gene}_Mutations.csv")
+      frameshift_number=$(echo "$frameshift_info" | awk -F', ' '{print $2}')
+      # Check if frameshifts are present and that the alignment has not failed
+      if [[ "$frameshift_number" != "0" && (! -f "$ErrorFile" || $(grep -c "${SequenceName_shell}_${gene}" "$ErrorFile") -eq 0) ]]; then
+        echo "$frameshift_info" >> Frameshifts.txt
+      fi
+    fi
+  done
+elif [[ "$Mutations" == "false" ]]; then
+  echo -e "${BLUE}To list frameshifts found in the sample enable the 'Mutations' virulign option.${END}"
+fi
+
+# Delete frameshift if no frameshifts are recorded
+if [[ -f "Frameshifts.txt"  ]] && [[ "$Mutations" == "true" ]]; then
+  if [[ "$( wc -l <Frameshifts.txt )" -eq 1 ]]; then
+      rm Frameshifts.txt
+      echo "No frameshifts found within successful alignments for $SequenceName_shell"
+  fi
+fi
+
+# Identify indels
+if [[ -f "Frameshifts.txt" ]]; then
+  OutputCSV="Frameshifts.csv"
+  for gene in "${genes[@]}"; do
+  GeneRef="ref_$gene"
+  SampleGene=$(find . -type f -name "temp_${SequenceName_shell}_${gene}_only.fasta")
+    if [[ "${!gene}" = true ]]; then
+      "$python" "$PythonFuncs" CategoriseIndels --InputFile "HIV_${gene}_Nucl_corrected.fasta" --OutputCSV "$OutputCSV" --Gene "${gene}" \
+      --SequenceName "${SequenceName_shell}" --ReferenceName "${!GeneRef}" --GeneCoordInfo "$GeneCoordInfo" --GenomeFile "$ReferenceFile" \
+      --AlignmentFile "$HXB2_Alignment" --ExtractedGeneFile "$SampleGene" || { echo "Problem finding indel positions. Quitting." >&2; exit 1; }
+    fi
+  done
+fi
+
+# Warn if some genes have missing coverage
+if [[ -s "MissingCoverage.txt" ]]; then
+  echo -e "${YELLOW}Some genes were not analysed due to missing coverage, check 'MissingCoverage.txt'.${END}"
+fi
+
+# Delete temporary files
+# Check that the directory is correct before deleting as a failsafe
+if [[ "$CC_DeleteTemp" == "true" ]]; then
+  CurrentDir=$(pwd)
+  if [[ "$CurrentDir" = "$OutputDir" ]]; then
+    rm ./temp_*
+    echo "Deleting temporary files. Set CC_DeleteTemp to false in config if choosing to keep these files."
+  else
+    echo "The current directory is not the expected Output Directory '$OutputDir'. Aborting deletion."
+  fi
+else
+  echo "Temporary files have not been deleted. To do so, set CC_DeleteTemp to true in the config."
+fi
diff --git a/bin/tools/CodonCorrectionInit.sh b/bin/tools/CodonCorrectionInit.sh
new file mode 100755
index 0000000..315edce
--- /dev/null
+++ b/bin/tools/CodonCorrectionInit.sh
@@ -0,0 +1,86 @@
+#!/usr/bin/env bash
+
+set -u
+set -o pipefail
+
+# Find shiver files
+ToolsDir=$(cd "$(dirname "${BASH_SOURCE[0]}" )" && pwd)
+echo $ToolsDir
+shiver_bin=$(dirname "$ToolsDir") # /path/to/shiver/bin
+source "$shiver_bin"/'config.sh'
+source "$shiver_bin"/'shiver_funcs.sh'
+PythonFuncs="$shiver_bin"/'tools/CC_Python_funcs.py'
+
+# This script is to be run once prior to the use of CodonCorrection.sh. The current version of the init assumes the presence of a whole genome 
+# reference file and a list of gene coordinates in the exact correct format - header included. 
+
+# Give specific description for gene coords
+GeneCoord_Header="Sequence_name, gag_start, gag_end, pol_start, pol_end, vif_start, vif_end, vpr_start, \
+vpr_end, vpu_start, vpu_end, env_start, env_end, nef_start, nef_end"
+
+UsageInstructions="Arguments for this script:
+(1) A fasta file of aligned annotatable references
+(2) The output folder for the BLAST database and init steps
+(3) A file of gene coordinates as a txt file, with the header: '$GeneCoord_Header'
+The gene coordinates for each sequence should be listed per line in the same order as the above header, separated by commas.
+"
+
+# Check correct arguments
+NumArgsExpected=3
+if [ "$#" -ne "$NumArgsExpected" ]; then
+  echo "$UsageInstructions"
+  echo "$#" 'arguments specified;' "$NumArgsExpected" 'expected. Quitting.' >&2
+  exit 1
+fi
+
+ReferenceFasta="$1"
+OutputDirInit="$2"
+GeneCoordInfo="$3"
+
+CheckFilesExist "$ReferenceFasta" "$GeneCoordInfo"
+
+# Check the output directory and cd
+if [[ -d "$OutputDirInit" ]]; then
+  echo "$OutputDirInit exists already; quitting to prevent overwriting." >&2
+  exit 1
+fi
+mkdir -p "$OutputDirInit" && cd "$OutputDirInit" ||
+{ echo "Could not mkdir then cd to $OutputDirInit. Quitting." >&2 ; exit 1 ; }
+
+# Check the reference file contains sequences
+if ! grep -e '^>' "$ReferenceFasta" > /dev/null; then
+  echo "Reference file $ReferenceFasta contains no sequences. Quitting." >&2
+  exit 1
+fi
+
+# Check GeneCoordInfo header is as expected
+  # Not strictly necessary for function but ensures the gene info is formatted in the correct way.
+GC_FirstLine=$(head -n 1 "$GeneCoordInfo")
+if [[ "$GC_FirstLine" != *"$GeneCoord_Header"* ]]; then
+  echo -e "Expected the gene coordinates file to have the header: '$GeneCoord_Header'\nPlease supply the gene coordinate \
+  data in the correct format and order. If coordinates are already supplied in the correct order, update the header to match. Quitting" >&2
+  exit 1
+fi
+
+# Extract each gene to make a BLAST database for each
+"$python" "$PythonFuncs" MakeReferenceDatabase --InitDir "$OutputDirInit" --GeneCoordInfo "$GeneCoordInfo" --GenomeFile "$ReferenceFasta" \
+|| { echo "Failed to extract the reference gene sequences. Quitting." >&2; exit 1; }
+
+# Copy reference file and gene coordinates file to working directory
+Ref_Copied="$OutputDirInit"/CC_References.fasta
+cp "$ReferenceFasta" "$Ref_Copied" || { echo "Failed to copy $ReferenceFasta to the output directory. Quitting." >&2; exit 1; }
+GeneCoords_Copied="$OutputDirInit"/CC_Coords.fasta
+cp "$GeneCoordInfo" "$GeneCoords_Copied" || { echo "Failed to copy $GeneCoordInfo to the output directory. Quitting." >&2; exit 1; }
+
+# Create a whole genome database to BLASTn to
+for gene in $genes; do
+  BLASTnDB="$OutputDirInit"/BLASTnDB_$gene
+  if [ ! -d "$BLASTnDB" ]; then
+    mkdir "$BLASTnDB"
+  fi || { echo "Unable to create database folder. Quitting."  >&2 ; exit 1 ; }
+
+  # Make the BLASTn database
+  GeneFile="$OutputDirInit/ReferenceGenes_$gene.fasta"
+  "$BlastDBcommand" -dbtype nucl -in "$GeneFile" -input_type fasta -out "$BLASTnDB/$gene" -logfile "$BLASTnDB/$gene.log" || { echo "Unable to create \
+  a blast database in $BLASTnDB. Check that the shiver config has the correct file path for 'BLASTDBcommand'. Quitting." ; exit 1; }
+done
diff --git a/bin/tools/test.sam b/bin/tools/test.sam
new file mode 100644
index 0000000..31503e4
--- /dev/null
+++ b/bin/tools/test.sam
@@ -0,0 +1,4 @@
+@HD	VN:1.3	SO:coordinate
+@SQ	SN:RefName	LN:10
+ReadName	99	RefName	1	47	10M	=	1	10	ACGTACGTAC	BBBBBBBBBB
+ReadName	147	RefName	1	47	10M	=	1	-10	ACGTACGTAC	BBBBBBBBBB