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JacobertsJacoberts
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New changes to docker local.
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‎backend/src/notebooks/jacob/paperplots/fig2_r1_tension.ipynb‎

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‎backend/src/notebooks/jacob/paperplots/fig2_r1_tension.svg‎

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‎backend/src/notebooks/jacob/paperplots/fig2_r1_tension_simplified.svg‎

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‎backend/src/notebooks/jacob/round1/template_plasmids/real_oplr_wt.gb‎

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LOCUS real_oplr_wt 6049 bp DNA circular SYN 10-OCT-2025
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DEFINITION pAP_OplR_CH_R3_0001.
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ACCESSION pAP_OplR_CH_R3_0001
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KEYWORDS .
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SOURCE
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ORGANISM .
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COMMENT Annotated with pLannotate v1.2.2.
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FEATURES Location/Qualifiers
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rep_origin 1..772
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/note="pLannotate"
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/database="snapgene"
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/identity="99.7"
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/match_length="100.3"
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/fragment="False"
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/other="rep_origin"
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/description="replication origin of the broad-host-range
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plasmid pBBR1 from Bordetella bronchiseptica; requires
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thepBBR1 Rep protein for replication"
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/label="pBBR1 oriV"
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CDS 773..1435
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/note="pLannotate"
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/database="snapgene"
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/identity="100.0"
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/match_length="100.0"
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/fragment="False"
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/other="CDS"
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/description="replication protein for the
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broad-host-rangeplasmid pBBR1 from Bordetella
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bronchiseptica"
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/label="pBBR1 Rep"
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CDS 1496..1555
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/note="pLannotate"
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/database="snapgene"
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/identity="100.0"
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/match_length="5.0"
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/fragment="True"
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/other="CDS"
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/description="tetracycline efflux protein; tet; confers
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resistance to tetracycline"
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/label="TcR (fragment)"
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terminator complement(1562..1589)
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/note="pLannotate"
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/database="snapgene"
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/identity="100.0"
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/match_length="100.0"
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/fragment="False"
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/other="terminator"
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/description="phage T7 early transcription terminator"
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/label="T7Te terminator"
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terminator complement(1605..1676)
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/note="pLannotate"
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/database="snapgene"
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/identity="100.0"
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/match_length="100.0"
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/fragment="False"
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/other="terminator"
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/description="transcription terminator T1 from the E.
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colirrnB gene"
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/label="rrnB T1 terminator"
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CDS complement(1709..2665)
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/created_by="jacobroberts"
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/label="oplr"
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misc_feature 1902..1903
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/Original_Bases="GT"
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/label="GT"
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/note="Geneious type: Editing History Replacement"
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misc_feature 2013..2014
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/Original_Bases="AG"
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/label="AG"
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/note="Geneious type: Editing History Replacement"
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misc_feature 2615..2616
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/Original_Bases="GG"
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/label="GG"
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/note="Geneious type: Editing History Replacement"
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promoter complement(2698..2715)
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/note="pLannotate"
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/database="snapgene"
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/identity="100.0"
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/match_length="51.4"
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/fragment="True"
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/other="promoter"
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/description="bacterial promoter (Registry of Standard
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Biological Parts BBa J23119) modified to end with an SpeI
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site"
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/label="J23119(SpeI) promoter (fragment)"
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terminator complement(2743..2837)
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/note="pLannotate"
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/database="snapgene"
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/identity="100.0"
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/match_length="100.0"
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/fragment="False"
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/other="terminator"
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/description="transcription terminator from phage lambda"
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/label="lambda t0 terminator"
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CDS complement(2871..3662)
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/note="pLannotate"
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/database="swissprot"
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/identity="100.0"
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/match_length="100.0"
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/fragment="False"
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/other="CDS"
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/description="Protein evidence at protein level:
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Swiss-Prot protein existence level 1. Resistance to
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kanamycin, neomycin, paromomycin, ribostamycin, butirosin
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and gentamicin B. From Klebsiella pneumoniae."
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/modified_by="jacobroberts"
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/label="marker"
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CDS complement(3694..3798)
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/note="pLannotate"
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/database="swissprot"
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/identity="94.3"
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/match_length="7.4"
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/fragment="True"
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/other="CDS"
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/description="Protein evidence at protein level:
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Swiss-Prot protein existence level 1. Mediates
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transposition of transposon Tn5 by a 'cut and paste'
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mechanism. First, the monomeric transposase binds the 19
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bp inverted DNA repeatsflanking the transposon. Then,
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dimerization of the DNA-bound transposase creates a
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synaptic DNA complex. After nicking of the first DNA
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strand, excision of the transposon proceeds through a
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series of intermediates. The transposase then mediates the
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insertion of the transposon at a new site by strand
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transfer. The activity of the wild-type transposase is
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very low, and is further inhibited by dimerization with
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the transposase inhibitor (inh). From Escherichia coli."
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/label="TN5P_ECOLX (fragment)"
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CDS 4025..4699
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/note="pLannotate"
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/database="fpbase"
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/identity="100.0"
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/match_length="100.0"
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/fragment="False"
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/other="CDS"
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/description
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/label="mRFP1"
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terminator 4735..4806
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/note="pLannotate"
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/database="snapgene"
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/identity="100.0"
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/match_length="100.0"
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/fragment="False"
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/other="terminator"
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/description="transcription terminator T1 from the E.
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colirrnB gene"
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/label="rrnB T1 terminator"
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terminator 4822..4849
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/note="pLannotate"
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/database="snapgene"
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/identity="100.0"
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/match_length="100.0"
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/fragment="False"
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/other="terminator"
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/description="phage T7 early transcription terminator"
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/label="T7Te terminator"
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ORIGIN
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1 gcggccaccg gctggctcgc ttcgctcggc ccgtggacaa ccctgctgga caagctgatg
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61 gacaggctgc gcctgcccac gagcttgacc acagggattg cccaccggct acccagcctt
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121 cgaccacata cccaccggct ccaactgcgc ggcctgcggc cttgccccat caattttttt
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181 aattttctct ggggaaaagc ctccggcctg cggcctgcgc gcttcgcttg ccggttggac
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241 accaagtgga aggcgggtca aggctcgcgc agcgaccgcg cagcggcttg gccttgacgc
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301 gcctggaacg acccaagcct atgcgagtgg gggcagtcga agggcgaagc ccgcccgcct
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361 gccccccgag cctcacggcg gcgagtgcgg gggttccaag ggggcagcgc caccttgggc
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421 aaggccgaag gccgcgcagt cgatcaacaa gccccggagg ggccactttt tgccggaggg
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481 ggagccgcgc cgaaggcgtg ggggaacccc gcaggggtgc ccttctttgg gcaccaaaga
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541 actagatata gggcgaaatg cgaaagactt aaaaatcaac aacttaaaaa aggggggtac
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601 gcaacagctc attgcggcac cccccgcaat agctcattgc gtaggttaaa gaaaatctgt
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661 aattgactgc cacttttacg caacgcataa ttgttgtcgc gctgccgaaa agttgcagct
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721 gattgcgcat ggtgccgcaa ccgtgcggca cccctaccgc atggagataa gcatggccac
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781 gcagtccaga gaaatcggca ttcaagccaa gaacaagccc ggtcactggg tgcaaacgga
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841 acgcaaagcg catgaggcgt gggccgggct tattgcgagg aaacccacgg cggcaatgct
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901 gctgcatcac ctcgtggcgc agatgggcca ccagaacgcc gtggtggtca gccagaagac
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961 actttccaag ctcatcggac gttctttgcg gacggtccaa tacgcagtca aggacttggt
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1021 ggccgagcgc tggatctccg tcgtgaagct caacggcccc ggcaccgtgt cggcctacgt
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1081 ggtcaatgac cgcgtggcgt ggggccagcc ccgcgaccag ttgcgcctgt cggtgttcag
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1141 tgccgccgtg gtggttgatc acgacgacca ggacgaatcg ctgttggggc atggcgacct
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1201 gcgccgcatc ccgaccctgt atccgggcga gcagcaacta ccgaccggcc ccggcgagga
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1261 gccgcccagc cagcccggca ttccgggcat ggaaccagac ctgccagcct tgaccgaaac
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1321 ggaggaatgg gaacggcgcg ggcagcagcg cctgccgatg cccgatgagc cgtgttttct
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1381 ggacgatggc gagccgttgg agccgccgac acgggtcacg ctgccgcgcc ggtagcactt
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1441 gggttgcgca gcaacccgta agtgcgctgt tccagactat cggctgtagc cgcctcgccg
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1501 ccctatacct tgtctgcctc cccgcgttgc gtcgcggtgc atggagccgg gccactataa
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1561 acgcagaaag gcccacccga aggtgagcca gtgtgactct agtagagagc gttcaccgac
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1621 aaacaacaga taaaacgaaa ggcccagtct ttcgactgag cctttcgttt tatttgatgc
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1681 ctggagatcc ttactcgagt ttggatcctc agtgcgtacg cgtagcccgc acttcgctcg
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1741 ccgtgcaccc atactgctgg cgaaacgcgc gggtgaattg cgcctggtcg gcaaaacccc
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1801 agcgaaatgc cagttcgccg atggccaggt ggcaatgcgg gtcgcgcagt tgccggtgca
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1861 cggcctccag gcgttgaagg cgtacccact cattaagggt gtagggcgtg atcgcgaaca
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1921 gcttgtgcag ataacgcagc gacagcccac aggcgccggc gatggtttgt ggcgacagct
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1981 cggggtcacc caggttttgc tgcacgtact gctcgacccg cgtcaggtgc agggtgctga
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2041 ggttgctgcc ttcgctgccc agcacgcgct catcctgctg caaggccagc agcagggtgg
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2101 cggaggcctg ttccagcagt aaatgccggg ctgccggggg gctggtgtcg aaatggcggg
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2161 cacacaggtc gagttgctcg acgaagatgc gccccaggcc ctgacgggcg tcgaagcaat
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2221 gccgggtata gcgcttgtgc cccagcaggt tggctttgag cgcacgctcg ggcagcttga
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2281 gcacccacaa gtcgttctgc gtgccgtagt ggaagcggta gggtgcatcg ccgcgctcga
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2341 cgatgaaacc gcccgggctg caactgatct ggtggccgtc ctgttcaaag tgcacctcgc
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2401 tgccatgcgg cacggtcacc aggtagaacg cttcatggtc ctggccgatg tgcgctttgc
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2461 tgcgtgagta acccagctgg ctggaccgca ggcgcgacag gctgagcggc gtgctcggcg
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2521 tactccagcg ctgcaggtgg ccatcgaacg gctgtccggc agcaaattca aggctcaatg
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2581 ggaaataggt gtcactgatg gcttcggccc agcgtacctg gcgctctggc tgtggccagc
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2641 cgtgggtcga gagttctgtg ggcatatgta tatctccttc ttaaagctag cataatccct
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2701 aggactgagc tagctatcag ctcgacctga atggaagctt ggattctcac caataaaaaa
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2761 cgcccggcgg caaccgagcg ttctgaacaa atccagatgg agttctgagg tcattactgg
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2821 atctatcaac aggagtccaa gcgagctctc gaaccccaga gtcccgctca gaagaactcg
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2881 tcaagaaggc gatagaaggc gatgcgctgc gaatcgggag cggcgatacc gtaaagcacg
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2941 aggaagcggt cagcccattc gccgccaagc tcttcagcaa tatcacgggt agccaacgct
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3001 atgtcctgat agcggtccgc cacacccagc cggccacagt cgatgaatcc agaaaagcgg
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3061 ccattttcca ccatgatatt cggcaagcag gcatcgccat gggtcacgac gagatcctcg
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3121 ccgtcgggca tgcgcgcctt gagcctggcg aacagttcgg ctggcgcgag cccctgatgc
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3181 tcttcgtcca gatcatcctg atcgacaaga ccggcttcca tccgagtacg tgctcgctcg
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3241 atgcgatgtt tcgcttggtg gtcgaatggg caggtagccg gatcaagcgt atgcagccgc
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3301 cgcattgcat cagccatgat ggatactttc tcggcaggag caaggtgaga tgacaggaga
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3361 tcctgccccg gcacttcgcc caatagcagc cagtcccttc ccgcttcagt gacaacgtcg
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3421 agcacagctg cgcaaggaac gcccgtcgtg gccagccacg atagccgcgc tgcctcgtcc
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3481 tgcagttcat tcagggcacc ggacaggtcg gtcttgacaa aaagaaccgg gcgcccctgc
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3541 gctgacagcc ggaacacggc ggcatcagag cagccgattg tctgttgtgc ccagtcatag
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3601 ccgaatagcc tctccaccca agcggccgga gaacctgcgt gcaatccatc ttgttcaatc
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3661 atgcgaaacg atcctcatcc tgtctcttga tcagatcatg atcccctgcg ccatcagatc
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3721 cttggcggca agaaagccat ccagtttact ttgcagggct tcccaacctt accagagggc
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3781 gccccagctg gcaattccga cgtcttgggg ccggccgggc aatggctggt gcgacagatg
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3841 ttggggcaat agttgtgtcg cctgcccgaa cttgaagtgc gcccagacac aacaaccggt
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3901 acacccagcg acaagccttc cccccacccc gccccttagc ctgtcaccac gcgccgcccc
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3961 gccgcggcac gcacctaaag cacaagaaca aacgttggtg accttttaag aaggagatat
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4021 acatatggcg agtagcgaag acgttatcaa agagttcatg cgtttcaaag ttcgtatgga
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4081 aggttccgtt aacggtcacg agttcgaaat cgaaggtgaa ggtgaaggtc gtccgtacga
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4141 aggtacccag accgctaaac tgaaagttac caaaggtggt ccgctgccgt tcgcttggga
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4201 catcctgtcc ccgcagttcc agtacggttc caaagcttac gttaaacacc cggctgacat
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4261 cccggactac ctgaaactgt ccttcccgga aggtttcaaa tgggaacgtg ttatgaactt
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4321 cgaagacggt ggtgttgtta ccgttaccca ggactcctcc ctgcaagacg gtgagttcat
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4381 ctacaaagtt aaactgcgtg gtaccaactt cccgtccgac ggtccggtta tgcagaaaaa
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4441 aaccatgggt tgggaagctt ccaccgaacg tatgtacccg gaagacggtg ctctgaaagg
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4501 tgaaatcaaa atgcgtctga aactgaaaga cggtggtcac tacgacgctg aagttaaaac
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4561 cacctacatg gctaaaaaac cggttcagct gccgggtgct tacaaaaccg acatcaaact
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4621 ggacatcacc tcccacaacg aagactacac catcgttgaa cagtacgaac gtgctgaagg
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4681 tcgtcactcc accggtgctt aaggatccaa actcgagtaa ggatctccag gcatcaaata
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4741 aaacgaaagg ctcagtcgaa agactgggcc tttcgtttta tctgttgttt gtcggtgaac
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4801 gctctctact agagtcacac tggctcacct tcgggtgggc ctttctgcgt ttatacctag
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4861 ggcgttcggc tgcggctggc gctgggcctg tttctggcgc tggacttccc gctgttccgt
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4921 cagcagcttt tcgcccacgg ccttgatgat cgcggcggcc ttggcctgca tatcccgatt
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4981 caacggcccc agggcgtcca gaacgggctt caggcgctcc cgaaggtctc gggccgtctc
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5041 ttgggcttga tcggccttct tgcgcatctc acgcgctcct gcggcggcct gtagggcagg
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5101 ctcatacccc tgccgaaccg cttttgtcag ccggtcggcc acggcttccg gcgtctcaac
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5161 gcgctttgag attcccagct tttcggccaa tccctgcggt gcataggcgc gtggctcgac
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5221 cgcttgcggg ctgatggtga cgtggcccac tggtggccgc tccagggcct cgtagaacgc
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5281 ctgaatgcgc gtgtgacgtg ccttgctgcc ctcgatgccc cgttgcagcc ctagatcggc
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5341 cacagcggcc gcaaacgtgg tctggtcgcg ggtcatctgc gctttgttgc cgatgaactc
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5401 cttggccgac agcctgccgt cctgcgtcag cggcaccacg aacgcggtca tgtgcgggct
249+
5461 ggtttcgtca cggtggatgc tggccgtcac gatgcgatcc gccccgtact tgtccgccag
250+
5521 ccacttgtgc gccttctcga agaacgccgc ctgctgttct tggctggccg acttccacca
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5581 ttccgggctg gccgtcatga cgtactcgac cgccaacaca gcgtccttgc gccgcttctc
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5641 tggcagcaac tcgcgcagtc ggcccatcgt ttcatcggtg ctgctggccg cccagtgctc
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5701 gttctctggc gtcctgctgg cgtcagcgtt gggcgtctcg cgctcgcggt aggcgtgctt
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5761 gagactggcc gccacgttgc ccattttcgc cagcttcttg catcgcatga tcgcgtatgc
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5821 cgccatgcct gcccctccct tttggtgtcc aaccggctcg acgggggcag cgcaaggcgg
256+
5881 tgcctccggc gggccactca atgcttgagt atactcacta gactttgctt cgcaaagtcg
257+
5941 tgaccgccta cggcggctgc ggcgccctac gggcttgctc tccgggcttc gccctgcgcg
258+
6001 gtcgctgcgc tcccttgcca gcccgtggat atgtggacga tggccgcga
259+
//

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