diff --git a/gene_sequences/script-problem1.sh b/gene_sequences/script-problem1.sh
new file mode 100644
index 0000000..88d5acf
--- /dev/null
+++ b/gene_sequences/script-problem1.sh
@@ -0,0 +1,23 @@
+#usage: bash script-problem1.sh
+#origin directory /afs/nd.edu/user30/poneil1/local/bin/IBC_EX11/gene_sequences
+
+#run each transporter file into an aligned sequence of their own and...
+#...combine these sequences into a single fasta file
+for transporter in transporter*.fasta
+do
+  	../../muscle -in $transporter -out transporterout.fasta
+        cat transporterout.fasta >> transporter-combined.fasta
+done
+#run the combined fasta file through muscle to align for final sequence
+../../muscle -in transporter-combined.fasta -out transporter-final.fasta
+
+#run each sporecoat file into an aligned sequence of their own and...
+#...combine these sequences into a single fasta file
+for sporecoat in sporecoat*
+do
+  	../../muscle -in $sporecoat -out sporecoatout.fasta
+        cat sporecoatout.fasta >> sporecoat-combined.fasta
+done
+
+#run the combined fasta file through muscle to align for final sequence
+../../muscle -in sporecoat-combined.fasta -out sporecoat-final.fasta
diff --git a/gene_sequences/script-problem2.sh b/gene_sequences/script-problem2.sh
new file mode 100644
index 0000000..7e17039
--- /dev/null
+++ b/gene_sequences/script-problem2.sh
@@ -0,0 +1,14 @@
+#Usage: bash script-problem2.sh
+#HMMer searches each transporter fasta with each proteome fasta
+#initial working directory: gene_sequences
+for transporter in transporter0*.fasta
+        do
+          	for proteome in ../proteomes/*
+                        do
+                          	echo $transporter >> sequence-hits.txt
+                                echo $proteome >> sequence-hits.txt
+                                ../../hmmbuild transporter.hmm $transporter
+                                ../../hmmsearch transporter.hmm $proteome | grep$
+                        done
+        done
+
diff --git a/gene_sequences/sequence-hits.txt b/gene_sequences/sequence-hits.txt
new file mode 100644
index 0000000..4b069b3
--- /dev/null
+++ b/gene_sequences/sequence-hits.txt
@@ -0,0 +1,352 @@
+transporter01.fasta
+../proteomes/Arthrobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter01.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter01.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter01.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter01.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter01.fasta
+../proteomes/Roseobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter02.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter02.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter02.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter02.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter02.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter02.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter03.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter03.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter03.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter03.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter03.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter03.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter04.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Bacillus.fasta
+1 
+transporter04.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter04.fasta
+../proteomes/Flavobacterium.fasta
+1 
+transporter04.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter04.fasta
+../proteomes/Rhizobium.fasta
+2 
+transporter04.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter01.fasta
+../proteomes/Arthrobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter01.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter01.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter01.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter01.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter01.fasta
+../proteomes/Roseobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter02.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter02.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter02.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter02.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter02.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter02.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter03.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter03.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter03.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter03.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter03.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter03.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter04.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Bacillus.fasta
+1 
+transporter04.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter04.fasta
+../proteomes/Flavobacterium.fasta
+1 
+transporter04.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter04.fasta
+../proteomes/Rhizobium.fasta
+2 
+transporter04.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter-combined.fasta
+../proteomes/Arthrobacter.fasta
+transporter-combined.fasta
+../proteomes/Bacillus.fasta
+transporter-combined.fasta
+../proteomes/Clostridium.fasta
+transporter-combined.fasta
+../proteomes/Flavobacterium.fasta
+transporter-combined.fasta
+../proteomes/Limnohabitans.fasta
+transporter-combined.fasta
+../proteomes/Rhizobium.fasta
+transporter-combined.fasta
+../proteomes/Roseobacter.fasta
+transporter-combined.fasta
+../proteomes/Verrucomicrobia.fasta
+transporter-final.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter-final.fasta
+../proteomes/Bacillus.fasta
+1 
+transporter-final.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter-final.fasta
+../proteomes/Flavobacterium.fasta
+1 
+transporter-final.fasta
+../proteomes/Limnohabitans.fasta
+1 
+transporter-final.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter-final.fasta
+../proteomes/Roseobacter.fasta
+1 
+transporter-final.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporterout.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporterout.fasta
+../proteomes/Bacillus.fasta
+1 
+transporterout.fasta
+../proteomes/Clostridium.fasta
+0 
+transporterout.fasta
+../proteomes/Flavobacterium.fasta
+1 
+transporterout.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporterout.fasta
+../proteomes/Rhizobium.fasta
+2 
+transporterout.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporterout.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter01.fasta
+../proteomes/Arthrobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter01.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter01.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter01.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter01.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter01.fasta
+../proteomes/Roseobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter02.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter02.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter02.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter02.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter02.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter02.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter03.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter03.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter03.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter03.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter03.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter03.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter04.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Bacillus.fasta
+1 
+transporter04.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter04.fasta
+../proteomes/Flavobacterium.fasta
+1 
+transporter04.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter04.fasta
+../proteomes/Rhizobium.fasta
+2 
+transporter04.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Verrucomicrobia.fasta
+0
diff --git a/gene_sequences/sporecoat-combined.fasta b/gene_sequences/sporecoat-combined.fasta
new file mode 100644
index 0000000..f9fa1da
--- /dev/null
+++ b/gene_sequences/sporecoat-combined.fasta
@@ -0,0 +1,104 @@
+>Q0AAK3_ALKEH/24160
+DTATFDVTATVDPTCTV-DADNLVFGTYDPFSDTPLDENSEIRVQCTSDTPYDIGLDDGD
+NTGAEGERRMAL----ADESDFLEYDLYHDNHGGTSWGDIDSGAELTGLSG----TGSEQ
+SYVVYGRIFAEQSVAVGNYVDTIEVT
+>Q8XPY6_RALSO/36170
+KTTTFTVSLTLQADCSI-SANALNFGTQGV-LAANVDQTATLSVTCSNTAPYNVGFDAGT
+TTGSTIAARLLA----GSGAATVGFQLYSDSARTQIWGNTVGTDTVSG-TG----SGTAQ
+VLTVYGRVPSQNSPAAGTYSTTITAT
+>Q63W79_BURPS/31169
+ATATFTVSLTIQANCTI-SANALSFGTNGV-LATAVNQQTTLSVTCSNTTSYNVGLDAGN
+VSGSTVSSRLLAGTTTGNTSTTVSFQLYQDSGHTTIWGNTVGTNTVSG-TG----NGTAQ
+TLSVYGQVPAQTTPKPDTYESTVTAT
+>Q0BSH7_GRABC/37169
+TTTTFQVTATVQASCII-QATNLSFGNY---SGSQTDATSTIQVTCTNSTPYNVGLSAGT
+GSGATVSNRKMS----LNSTSALPYALYSDASRSTNWGNTPNQDTVSG-TG----NGSAQ
+SLTVYGRIQTGNYPTPGSYADTITAT
+>Q8XVY0_RALSO/26164
+TTTTFSVSTTVNATCVINSASALTFAAFDP-SQGAQASTSSISVNCTNTTPFNIGLNAGT
+GTGATVASRVMT-----SGANTLTYSLYQDSGHASVWGNTVGTNTVAG-TGAGMAAGNAI
+TKTVYGLIPSQPNTVPGNYADTVTVT
+>Q8XVY3_RALSO/23163
+VLVALASWAPGALAVSCSV-SANALSFGAYNT-----TSNLTGTTTVTITCGAWG-GASS
+INYTLSASVGSGTYA-NRQVLN-GSNVIAYNLYTTSADTSIWGDGN-GD------GTVTL
+SGTVTKQVGTVNLTIYGKIN-GGQNVVPGSYATTIPIT
+>Q8XPY9_RALSO/25163
+-----------ASAQSCSV-ASASLNFGSISPVQ---AGNTDTSTTLTVSCSGFLLQGTV
+ARACLNLGVGSGDTGISPRVLSAGANQLQYNLYADSARSVVWGGRTTPATPAIQVDVSLG
+LLGFGSA----TVTVYGRVPGGQTTVPAGAYTQSFSGT
+>A7H7Q6_ANADF/25150
+ATAQFQ--VTATVVKKCKI-SATTIAFGNYDP-----ATILSAEGTLTLKCT----KGTL
+YSVALDGGSTGS-----RQMTQ-AAEVLDYELYSDAGHTAVWPSTA---------AAPSV
+AAAGADE----ALIIFAQVP-ADQYPAPGAYADTVTAT
+>Q2IFL0_ANADE/27162
+ATATLD--VTATVVPSCTI-AATPVAFGSYDPLVTNAATALDAQGTVTVTCT----TGTA
+YTVGLGAGNSGSGSRAMQHASI-AGAQLPYELYQEAARTTVWDSTV----------MQAG
+TAASITP---VQYTVYGRIP-AAQNVPTGNYADAVVAT
+>Q0C623_HYPNA/23151
+ANGTLD--VQATVVNTCVV-LTAPVVFASVGL------DEVTANGSITVNCT----NTSA
+FTVALDGGDSGDISARSLTHAS-LPASFNYQLYTDAGLTTVWGDGVTGS------Q---A
+NGSGPSQ----TLTVYGRT--TSTPDTAGAYADEVQVT
+>Q7CVQ4_AGRFC/27162
+ATTNFN--VQITIQAACQINSAGNLDFGTNGVI----GAPIDVTSQIVVQCT----ASTP
+FSLGLSAGAGSGATVANRLMTSAAGATISYSLYTTAAHSTVWGNTV-GT------DRQTG
+TGTGAPQ----NFTVFGRVP-AQTTPAVGVYTDTVTAT
+>Q985D5_RHILO/27162
+ATGNMT--VRITIQAECKVQTATDMDFGTNGVI----DANVDQTSTISVQCT----NSTP
+YNVGLSAGVGAGATVAVRKMTGPAAAVLNYSLYRDVARAQLWGTTI-GT------DTVAG
+TGNGAAQ----PLTVYGRVP-PQTTPGAGVYTDTVAIT
+>A6X8A6_OCHA4/27162
+ATGNMN--VRITIQAECKIVTATDLDFGTKGVI----DVNVDQTSTISVQCT----NGTP
+YTVGLSAGGGAGATVAMRKMTGAASATINYTIYRDAARTQVWGVTA-GT------DVVSG
+TGNGNAQ----SITAYGRVP-AQTTPAPGVYSDVVSVT
+>Q63W78_BURPS/193326
+-TFAFT--ASATVVNDCFI-NATNVAFGSTGVI----QGALTATGTISAQCT----NGDA
+FRIALNGGASGNVAARAMQRTG-GGGAVNYQLYLDAAHSTIWGDGTAGT------STATG
+TGSGLSQ----SLTVYGQVP-AQTTPAPGTYSDTITAT
+>A9CH19_AGRFC/182313
+TQVPFT--VSAAVAPTCII-SAQNINFGSHGVL----NTAVDANGAINLTCT----NGLN
+YSVALNGGLSNSPPA-ARQMVQ-GAASIIYGLYRDVSRTNVWGSAA-G-------QIATG
+TGNGSLQ----TLTVFGRVP-AQNTPAPGNYADTVVVT
+>Q985D8_RHILO/205338
+DRPTFT--INAIVPANCLL-AIQNIDFGSNGIL----GANVDATGGVSITCT----PGTP
+YTVSLSNGTTGSAPT-ARKMSK-GVETVTYGLYKDNARSQVWGDAAMPG------STVAG
+SGSGAAQ----NLTIYGRVP-AQTTPSAGVYTDTVVVT
+>Q3A2W0_PELCD/10150
+IIVLLFAVDAYAFHCEVTTTPVSFGAYDVFSSFSLDTTGRISVSCNNPEKKRMPVTISIS
+RGAANSFSPRQMRR-IGGSDRMDYYLFVDASRTAVWGDGTGGSSTYVGMIDRTSPL----
+--NVPIYGRIPARQNLRA-GSYQDILVVT
+>A9CH19_AGRFC/11158
+IAAAFVASPVLAQSCTFSMSDMNFGFVNLAGGAAVDTTATLSVTCNNPLSLALSIRICPN
+INAGGGGQSGGIRRMLQGSNILNYQLYQTSARTTAWGSVTQPALGAPPPIDMALPLL-IN
+STTRTVYGRINAGQASAARGLYLSSFAGG
+>Q985D8_RHILO/37183
+SAALLLPTVAWAQSCSFGVSAMNFGLVDTLSGSSSNSTATLSVNCTGLLLQR--ILVCPN
+LGTGSGGATASARQMLSGANDLNYQLYSDSARSVVWGSYAWPYPPTAPGFALTLNVLGSG
+SASQTIYGAILGGQATAVPSTYLSTFSGS
+>Q12FX3_POLSJ/50194
+TWGVLLAAGTAHATISCSVS---GNGFTSVYDPIS-----TVP-NDNVSSVTINC-SRAS
+GDPTTTTYSLASTNGLYPQGQ-NNRAYY---PTNKYLKYDIYKDAAYSSRWGPG--GSAP
+FTGTLNFGSGTSASLTLP-YYNRVAAQQS-AVAADYTDTMTAT
+>A1VIJ0_POLNA/19170
+ALFLLLATAGPAQAGSCTVGSS-GLAFGA-YQPLTFAGKLTSSAVTSNASISVVCTGIAS
+GGA----YSIALGPSTTGSGDRISTRYLGNSNGGDDMSFNIYTSASYSTVWGNGTTGGLV
+GG---SI-PVGDSNQSQP-VYGRIAASQNTLRAGSYSGSLTMT
+>Q60C08_METCA/20167
+--LLACPKISDADPYQCDIGNI-SVPHAV-YDPTD-----SNPNSSGVGTVGITCHLKNA
+KQTQQVQYTIALSRG--SSGSYNPRRMS---GGRGSLGYNLYLDAARVTIWGDGSGGTFP
+LRGTLLLNPTTPVQQVIHNIYGLIPPLQD-VYAGTYTDTVTIT
+>Q1D5L1_MYXXD/13153
+AVAGVCGLLPGLAGAVCQIRSTIGVSFGT-YLTTD-----LLP-RDSAGSITYRCEGQIT
+PIT------IDFSAG--GSGTPLARSMAG--PGAQRLEYNLYVDATRLIVWGNGTSGTGR
+YG---PVVPLFGVEVTVP-IFGRIPAGQA-IPAGAYADTVVMT
+>Q0AAK6_ALKEH/8153
+SLFLVAAGSGSAQAYTCSISAD-PLAFGQ-YDPIT-----GAQ-VDGASEVSVSC-SLLG
+LVSLLVSYEISLDPG--TGGSYHPRALS---SATDTLDYNLYVDTARTEIWGDGTDDTAT
+VTDSYTL-GVLTVTRYYP-VYGRVFADQN-VAAGVYDDTITAT
+>A7H7Q5_ANADF/16150
+APRAVDAAQPPSPGPSCSVSAG-SVAFGA-YDPLS-----PTH-LDSTGTIGLTC-AVRQ
+LVT------ISLGTG--QSGT-FARELRG--PGGAALRYDLYTDATRTQVWGDGTAGTAT
+WP------FETERGRYVP-VYARVLAGQD-VPAGPYSDTIVVT
+>Q2IFK8_ANADE/19157
+ATALSLVAPAAARAASCSLTMGTSIAFGA-YDPLS-----PVP-LTTTGMLQYRC-SRGQ
+PIR------ITFTAG--SSGDVYARTLR---QGPWTLAYNLYADAGFGTVWGDGTGGTAA
+AP---AV-TTLSNGLTVAYVFGRIPARQE-PPVGPYSDTIVVT
diff --git a/gene_sequences/sporecoat-final.fasta b/gene_sequences/sporecoat-final.fasta
new file mode 100644
index 0000000..1f2fec3
--- /dev/null
+++ b/gene_sequences/sporecoat-final.fasta
@@ -0,0 +1,104 @@
+>Q12FX3_POLSJ/50194
+TWGVLLAAGTAHATISCSV-SGNGFT-SVYDPIS------TVPNDNVSSVTINCS-R---
+-ASGDPTTTTYSLASTNGLYPQGQNNRAY--YPTNKYLKYDIYKDAAYSSRWGPG--GSA
+PFTG--TLNFGSGTSASLTLPYYNRVAA-QQSAVAADYTDTMTAT
+>Q60C08_METCA/20167
+LLACPKIS--DADPYQCDI-GNISVPHAVYDPTDS-----NPNSSGVGTVGITCHLKNAK
+QTQQVQYTIALSRGSSGSYNP--RRMSG-----GRGSLGYNLYLDAARVTIWGDGSGGTF
+PLRGTLLLNPTTPVQQVIHN-IYGLIPP-LQDVYAGTYTDTVTIT
+>A9CH19_AGRFC/11158
+IAAAFVAS--PVLAQSCTF-SMSDMNFGFVNLAG------GAAVDTTATLSVTCN-NPLS
+LALSIRICPNINAGGGGQSGGIRRMLQ------GSNILNYQLYQTSARTTAWGSVTQPAL
+GAPPPIDMALPLLINSTTRT-VYGRINAGQASAARGLYLSSFAGG
+>Q985D8_RHILO/37183
+SAALLLPT--VAWAQSCSF-GVSAMNFGLVDTLS------GSSSNSTATLSVNCT-GLLL
+QR--ILVCPNLGTGSGGATASARQMLS------GANDLNYQLYSDSARSVVWGSYAWPYP
+PTAPGFALTLNVLGSGSASQTIYGAILGGQATAVPSTYLSTFSGS
+>Q8XPY9_RALSO/25163
+-----------ASAQSCSV-ASASLNFGSISPVQ------AGNTDTSTTLTVSCS-GFLL
+QG--TVARACLNLGVGSGDTGISPRVLSA----GANQLQYNLYADSARSVVWGGRTTPAT
+PAIQ-VDVSLGLLGFGSATVTVYGRVPGGQTTVPAGAYTQSFSGT
+>Q8XVY3_RALSO/23163
+VLVALASWAPGALAVSCSV-SANALSFGAYNT--------TSNLTGTTTVTITCG-A---
+WGGASSINYTLSASVGSGTYANRQVLN------GSNVIAYNLYTTSADTSIWGDGN-GDG
+TVTL--SGTVTKQVGTVNLT-IYGKING-GQNVVPGSYATTIPIT
+>A1VIJ0_POLNA/19170
+ALFLLLATAGPAQAGSCTV-GSSGLAFGAYQPLTFAGKLTSSAVTSNASISVVCT-GIAS
+GG---AYSIALGPSTTGSGDRISTRYLGN--SNGGDDMSFNIYTSASYSTVWGNGTTG-G
+LVGG--SIPVG--DSNQSQP-VYGRIAASQNTLRAGSYSGSLTMT
+>Q0AAK6_ALKEH/8153
+SLFLVAAGSGSAQAYTCSI-SADPLAFGQYDPIT------GAQVDGASEVSVSCS-LLGL
+VSLLVSYEISLDPGTGGSYHPRALSS-------ATDTLDYNLYVDTARTEIWGDGTDDTA
+TVTD--SYTLGVLTVTRYYP-VYGRVFA-DQNVAAGVYDDTITAT
+>Q1D5L1_MYXXD/13153
+AVAGVCGLLPGLAGAVCQIRSTIGVSFGTYLTTD------LLPRDSAGSITYRCE-G---
+QI--TPITIDFSAGGSG--TPLARSMAGP----GAQRLEYNLYVDATRLIVWGNGTSGTG
+RYGP--VVPLF--GVEVTVP-IFGRIPA-GQAIPAGAYADTVVMT
+>Q3A2W0_PELCD/10150
+IIVLLFAV--DAYAFHCEV-TTTPVSFGAYDVFS------SFSLDTTGRISVSCN-NPEK
+KR--MPVTISISRGAANSFSPRQMRRIG-----GSDRMDYYLFVDASRTAVWGDGTGGSS
+TYVG--MIDR---TSPLNVP-IYGRIPA-RQNLRAGSYQDILVVT
+>Q0C623_HYPNA/23151
+ANGTLDVQ--ATVVNTCVV-LTAPVVFASVG---------LDEVTANGSITVNCT-N---
+-T--SAFTVALDGGDSGDISARSLTHAS-----LPASFNYQLYTDAGLTTVWGDGVTGSQ
+ANGS---------GPSQTLT-VYGRTTS-TPDTA-GAYADEVQVT
+>A7H7Q5_ANADF/16150
+APRAVDAAQPPSPGPSCSV-SAGSVAFGAYDPLS------PTHLDSTGTIGLTCA-V---
+-R--QLVTISLGTGQSG---TFARELRGP----GGAALRYDLYTDATRTQVWGDGTAGTA
+TWPF--ET-----ERGRYVP-VYARVLA-GQDVPAGPYSDTIVVT
+>Q2IFK8_ANADE/19157
+ATALSLVAPAAARAASCSLTMGTSIAFGAYDPLS------PVPLTTTGMLQYRCS-R---
+-G--QPIRITFTAGSSGDVYARTLRQ-------GPWTLAYNLYADAGFGTVWGDGTGGTA
+AAPA--VTTL---SNGLTVAYVFGRIPA-RQEPPVGPYSDTIVVT
+>Q0AAK3_ALKEH/24160
+DTATFDVT--ATVDPTCTV-DADNLVFGTYDPFS------DTPLDENSEIRVQCT-S---
+-D--TPYDIGLDDGDNTGAEGERRMALAD----ESDFLEYDLYHDNHGGTSWGDIDSGAE
+LTGL--SGT----GSEQSYV-VYGRIFA-EQSVAVGNYVDTIEVT
+>A7H7Q6_ANADF/25150
+ATAQFQVT--ATVVKKCKI-SATTIAFGNYDP--------ATILSAEGTLTLKCT-K---
+-G--TLYSVALDGGSTG-----SRQMTQ-----AAEVLDYELYSDAGHTAVWPSTAAAPS
+VAAA---------GADEALI-IFAQVPA-DQYPAPGAYADTVTAT
+>Q2IFL0_ANADE/27162
+ATATLDVT--ATVVPSCTI-AATPVAFGSYDPLVTN---AATALDAQGTVTVTCT-T---
+-G--TAYTVGLGAGNSGSGSRAMQHASI-----AGAQLPYELYQEAARTTVWDSTVMQAG
+TAAS---------ITPVQYT-VYGRIPA-AQNVPTGNYADAVVAT
+>Q985D8_RHILO/205338
+DRPTFTIN--AIVPANCLL-AIQNIDFGSNGIL-------GANVDATGGVSITCT-P---
+-G--TPYTVSLSNGT-TGSAPTARKMSK-----GVETVTYGLYKDNARSQVWGDAAMPGS
+TVAG--SGS----GAAQNLT-IYGRVPA-QTTPSAGVYTDTVVVT
+>Q8XVY0_RALSO/26164
+TTTTFSVS--TTVNATCVINSASALTFAAFDPS-------QGAQASTSSISVNCT-N---
+-T--TPFNIGLNAGTGTGATVASRVMTS-----GANTLTYSLYQDSGHASVWGN-TVGTN
+TVAG--TGAGMAAGNAITKT-VYGLIPS-QPNTVPGNYADTVTVT
+>Q0BSH7_GRABC/37169
+TTTTFQVT--ATVQASCII-QATNLSFGNYS---------GSQTDATSTIQVTCT-N---
+-S--TPYNVGLSAGTGSGATVSNRKMSLN----STSALPYALYSDASRSTNWGN-TPNQD
+TVSG--TGN----GSAQSLT-VYGRIQT-GNYPTPGSYADTITAT
+>Q8XPY6_RALSO/36170
+KTTTFTVS--LTLQADCSI-SANALNFGTQGVL-------AANVDQTATLSVTCS-N---
+-T--APYNVGFDAGTTTGSTIAARLLAGS----GAATVGFQLYSDSARTQIWGN-TVGTD
+TVSG--TGS----GTAQVLT-VYGRVPS-QNSPAAGTYSTTITAT
+>Q63W79_BURPS/31169
+ATATFTVS--LTIQANCTI-SANALSFGTNGVL-------ATAVNQQTTLSVTCS-N---
+-T--TSYNVGLDAGNVSGSTVSSRLLAGTTTGNTSTTVSFQLYQDSGHTTIWGN-TVGTN
+TVSG--TGN----GTAQTLS-VYGQVPA-QTTPKPDTYESTVTAT
+>Q7CVQ4_AGRFC/27162
+ATTNFNVQ--ITIQAACQINSAGNLDFGTNGVI-------GAPIDVTSQIVVQCT-A---
+-S--TPFSLGLSAGAGSGATVANRLMTSA----AGATISYSLYTTAAHSTVWGN-TVGTD
+RQTG--TGT----GAPQNFT-VFGRVPA-QTTPAVGVYTDTVTAT
+>Q985D5_RHILO/27162
+ATGNMTVR--ITIQAECKVQTATDMDFGTNGVI-------DANVDQTSTISVQCT-N---
+-S--TPYNVGLSAGVGAGATVAVRKMTGP----AAAVLNYSLYRDVARAQLWGT-TIGTD
+TVAG--TGN----GAAQPLT-VYGRVPP-QTTPGAGVYTDTVAIT
+>A6X8A6_OCHA4/27162
+ATGNMNVR--ITIQAECKIVTATDLDFGTKGVI-------DVNVDQTSTISVQCT-N---
+-G--TPYTVGLSAGGGAGATVAMRKMTGA----ASATINYTIYRDAARTQVWGV-TAGTD
+VVSG--TGN----GNAQSIT-AYGRVPA-QTTPAPGVYSDVVSVT
+>A9CH19_AGRFC/182313
+TQVPFTVS--AAVAPTCII-SAQNINFGSHGVL-------NTAVDANGAINLTCT-N---
+-G--LNYSVALNGGLSNS-PPAARQMVQ-----GAASIIYGLYRDVSRTNVW--GSAAGQ
+IATG--TGN----GSLQTLT-VFGRVPA-QNTPAPGNYADTVVVT
+>Q63W78_BURPS/193326
+-TFAFTAS--ATVVNDCFI-NATNVAFGSTGVI-------QGALTATGTISAQCT-N---
+-G--DAFRIALNGGASGNVAARAMQRTG-----GGGAVNYQLYLDAAHSTIWGDGTAGTS
+TATG--TGS----GLSQSLT-VYGQVPA-QTTPAPGTYSDTITAT
diff --git a/gene_sequences/sporecoatout.fasta b/gene_sequences/sporecoatout.fasta
new file mode 100644
index 0000000..d38c594
--- /dev/null
+++ b/gene_sequences/sporecoatout.fasta
@@ -0,0 +1,10 @@
+LVSLLVSYEISLDPG--TGGSYHPRALS---SATDTLDYNLYVDTARTEIWGDGTDDTAT
+VTDSYTL-GVLTVTRYYP-VYGRVFADQN-VAAGVYDDTITAT
+>A7H7Q5_ANADF/16150
+APRAVDAAQPPSPGPSCSVSAG-SVAFGA-YDPLS-----PTH-LDSTGTIGLTC-AVRQ
+LVT------ISLGTG--QSGT-FARELRG--PGGAALRYDLYTDATRTQVWGDGTAGTAT
+WP------FETERGRYVP-VYARVLAGQD-VPAGPYSDTIVVT
+>Q2IFK8_ANADE/19157
+ATALSLVAPAAARAASCSLTMGTSIAFGA-YDPLS-----PVP-LTTTGMLQYRC-SRGQ
+PIR------ITFTAG--SSGDVYARTLR---QGPWTLAYNLYADAGFGTVWGDGTGGTAA
+AP---AV-TTLSNGLTVAYVFGRIPARQE-PPVGPYSDTIVVT
diff --git a/gene_sequences/transporter-combined.fasta b/gene_sequences/transporter-combined.fasta
new file mode 100644
index 0000000..70f4629
--- /dev/null
+++ b/gene_sequences/transporter-combined.fasta
@@ -0,0 +1,32 @@
+>LACY_CITFR/1412
+MYYLKNTNFWMFGFFFFFYFFIMGAYFPFFPIWLHEVNHISKGDTGIIFACISLFSLLFQ
+PIFGLLSDKLGLRKHLLWVITGMLVMFAPFFIYVFGPLLQVNILLGSIVGGIYLGFIYNA
+GAPAIEAYIEKASRRSNFEFGRARMFGCVGWALCASIAGIMFTINNQFVFWLGSGCAVIL
+ALLLLFSKTDVPSSAKVADAVGANNSAFSLKLALELFKQPKLWLISLYVVGVSCTYDVFD
+QQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIVNRIGGKNALLLAGTIMS
+VRIIGSHSHTALEVVILKTLHMFEIPFLIVGCFKYITSQFEVRFSATIYLVCFCFFKQLA
+MIFMSVLAGKMYESIGFQGAYLVLGIIRVSFTLISVFTLSGPGPFSLLRRRE
+>LACY_KLEOX/6416
+LAPRERHNFIYFMLFFFFYYFIMSAYFPFFPVWLAEVNHLTKTETGIVFSCISLFAIIFQ
+PVFGLISDKLGLRKHLLWTITILLILFAPFFIFVFSPLLQMNIMAGALVGGVYLGIVFSS
+RSGAVEAYIERVSRANRFEYGKVRVSGCVGWALCASITGILFSIDPNITFWIASGFALIL
+GVLLWVSKPESSNSAEVIDALGANRQAFSMRTAAELFRMPRFWGFIIYVVGVASVYDVFD
+QQFANFFKGFFSSPQRGTEVFGFVTTGGELLNALIMFCAPAIINRIGAKNALLIAGLIMS
+VRILGSSFATSAVEVIILKMLHMFEIPFLLVGTFKYISSAFKGKLSATLFLIGFNLSKQL
+SSVVLSAWVGRMYDTVGFHQAYLILGCITLSFTVISLFTLKGSKTLLPATA
+>RAFB_ECOLX/4415
+ASTHKNTDFWIFGLFFFLYFFIMATCFPFLPVWLSDVVGLSKTDTGIVFSCLSLFAISFQ
+PLLGVISDRLGLKKNLIWSISLLLVFFAPFFLYVFAPLLHLNIWAGALTGGVFIGFVFSA
+GAGAIEAYIERVSRSSGFEYGKARMFGCLGWALCATMAGILFNVDPSLVFWMGSGGALLL
+LLLLYLARPSTSQTAMVMNALGANSSLISTRMVFSLFRMRQMWMFVLYTIGVACVYDVFD
+QQFAIFFRSFFDTPQAGIKAFGFATTAGEICNAIIMFCTPWIINRIGAKNTLLVAGGIMT
+IRITGSAFATTMTEVVILKMLHALEVPFLLVGAFKYITGVFDTRLSATVYLIGFQFSKQL
+AAILLSTFAGHLYDRMGFQNTYFVLGMIVLTVTVISAFTLSSSPGIVHPSVE
+>A0A026RKY7_ECOLX/4411
+NIPFRNAYYRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFM
+MFYGIVQDKLGLKKPLIWCMSFILVLTGPFMIYVYEPLLQSNFSVGLILGALFFGLGYLA
+GCGLLDSFTEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVF
+MMINMRFKDKDHQCIAADAGGVKKEDFIAVFKDRNFWVFVIFIVGTWSFYNIFDQQLFPV
+FYAGLFESHDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIMALRILS
+CALFVNPWIISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASSLGIVLL
+STPTGILFDHAGYQTVFFAISGIVCLMLLFGIFFLSKKREQIVMETPV
diff --git a/gene_sequences/transporter-final.fasta b/gene_sequences/transporter-final.fasta
new file mode 100644
index 0000000..2f47110
--- /dev/null
+++ b/gene_sequences/transporter-final.fasta
@@ -0,0 +1,32 @@
+>A0A026RKY7_ECOLX/4411
+NIPFRNAYYRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFM
+MFYGIVQDKLGLKKPLIWCMSFILVLTGPFMIYVYEPLLQSNFSVGLILGALFFGLGYLA
+GCGLLDSFTEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVF
+-MMINMRFKDKDHQCIAADAGGVKKEDF-----IAVFKDRNFWVFVIFIVGTWSFYNIFD
+QQLFPVFYAGLFESHDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIM
+ALRILSCALFVNPWIISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASS
+LGIVLLSTPTGILFDHAGYQTVFFAISGIVCLMLLFGIFFLSKKREQIVMETPV
+>RAFB_ECOLX/4415
+ASTHKNTDFWIFGLFFFLYFFIMATCFPFLPVWLSDVVGLSKTDTGIVFSCLSLFAISFQ
+PLLGVISDRLGLKKNLIWSISLLLVFFAPFFLYVFAPLLHLNIWAGALTGGVFIGFVFSA
+GAGAIEAYIERVSRSSGFEYGKARMFGCLGWALCATMAGILFNVDPSLVFWMGSGGALLL
+LLLLYLARPSTSQTAMVMNALGANSSLISTRMVFSLFRMRQMWMFVLYTIGVACVYDVFD
+QQ-FAIFFRSFFDTPQAGIKAFGFATTAGEICNAIIMFCTPWIINRIGAKNTLLVAGGIM
+TIRITGSAFATTMTEVVILKMLHALEVPFLLVGAFKYITGVFDTRLSATVYLIGFQFSKQ
+LAAILLSTFAGHLYDRMGFQNTYFVLGMIVLTVTVISAFTLS-SSPGIVHPSVE
+>LACY_CITFR/1412
+MYYLKNTNFWMFGFFFFFYFFIMGAYFPFFPIWLHEVNHISKGDTGIIFACISLFSLLFQ
+PIFGLLSDKLGLRKHLLWVITGMLVMFAPFFIYVFGPLLQVNILLGSIVGGIYLGFIYNA
+GAPAIEAYIEKASRRSNFEFGRARMFGCVGWALCASIAGIMFTINNQFVFWLGSGCAVIL
+ALLLLFSKTDVPSSAKVADAVGANNSAFSLKLALELFKQPKLWLISLYVVGVSCTYDVFD
+QQ-FANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIVNRIGGKNALLLAGTIM
+SVRIIGS-HSHTALEVVILKTLHMFEIPFLIVGCFKYITSQFEVRFSATIYLVCFCFFKQ
+LAMIFMSVLAGKMYESIGFQGAYLVLGIIRVSFTLISVFTLSGPGPFSLLRRRE
+>LACY_KLEOX/6416
+LAPRERHNFIYFMLFFFFYYFIMSAYFPFFPVWLAEVNHLTKTETGIVFSCISLFAIIFQ
+PVFGLISDKLGLRKHLLWTITILLILFAPFFIFVFSPLLQMNIMAGALVGGVYLGIVFSS
+RSGAVEAYIERVSRANRFEYGKVRVSGCVGWALCASITGILFSIDPNITFWIASGFALIL
+GVLLWVSKPESSNSAEVIDALGANRQAFSMRTAAELFRMPRFWGFIIYVVGVASVYDVFD
+QQ-FANFFKGFFSSPQRGTEVFGFVTTGGELLNALIMFCAPAIINRIGAKNALLIAGLIM
+SVRILGSSFATSAVEVIILKMLHMFEIPFLLVGTFKYISSAFKGKLSATLFLIGFNLSKQ
+LSSVVLSAWVGRMYDTVGFHQAYLILGCITLSFTVISLFTL--KGSKTLLPATA
diff --git a/gene_sequences/transporterout.fasta b/gene_sequences/transporterout.fasta
new file mode 100644
index 0000000..5649f92
--- /dev/null
+++ b/gene_sequences/transporterout.fasta
@@ -0,0 +1,8 @@
+>A0A026RKY7_ECOLX/4411
+NIPFRNAYYRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFM
+MFYGIVQDKLGLKKPLIWCMSFILVLTGPFMIYVYEPLLQSNFSVGLILGALFFGLGYLA
+GCGLLDSFTEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVF
+MMINMRFKDKDHQCIAADAGGVKKEDFIAVFKDRNFWVFVIFIVGTWSFYNIFDQQLFPV
+FYAGLFESHDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIMALRILS
+CALFVNPWIISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASSLGIVLL
+STPTGILFDHAGYQTVFFAISGIVCLMLLFGIFFLSKKREQIVMETPV