# HG changeset patch
# User rnateam
# Date 1438383637 14400
# Node ID 95526e9e38083cfb0e14449a21060b8adfe1a359
# Parent  8817d3a35fac3f4b1329c2bd590901868a5d0fe4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit c4313fc798bb8d55e27da78a3fa5d9774b95aaf7-dirty

diff -r 8817d3a35fac -r 95526e9e3808 mafft.xml
--- a/mafft.xml	Tue Jun 16 10:54:16 2015 -0400
+++ b/mafft.xml	Fri Jul 31 19:00:37 2015 -0400
@@ -16,20 +16,23 @@
     <![CDATA[
         #if $cond_flavour.flavourType != 'custom'
             $cond_flavour.flavourType
-        #else
+        #elif $cond_flavour.flavourType == 'custom'
             ### full parameter options
             mafft
         #end if
         
-        #if $cond_outformat.outputFormat == 'clustalw'
+        ## specify threads to use
+        --thread \${GALAXY_SLOTS:-1}
+        
+        #if $outputFormat.value == 'clustalw'
             --clustalout
         #end if
         
         $inputSequences > 
         
-        #if $cond_outformat.outputFormat == 'fasta'
+        #if $outputFormat.value == 'fasta'
             $outputFasta
-        #else ## $cond_outformat.outputFormat == 'clustalw'
+        #elif $outputFormat.value == 'clustalw'
             $outputClustalW
         #end if
     ]]>
@@ -39,6 +42,7 @@
         <conditional name="cond_flavour">
             <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.">
                 <option value="mafft-fftns" selected="true">fftns</option>
+                <option value="mafft --auto">auto</option>
                 <option value="mafft-fftnsi">fftnsi</option>
                 <option value="mafft-nwns">nwns</option>
                 <option value="mafft-nwnsi">nwnsi</option>
@@ -47,9 +51,10 @@
                 <option value="mafft-linsi">linsi</option>
                 <option value="mafft-qinsi">qinsi</option>
                 <option value="mafft-xinsi">xinsi</option>
-                <option value="custom">Custom Parameters</option>
+                <!-- <option value="custom">Custom Parameters</option> this should trigger tweaking of all parameters -->
             </param>
             <when value="mafft-fftns"/>
+            <when value="mafft --auto"/>
             <when value="mafft-fftnsi"/>
             <when value="mafft-nwns"/>
             <when value="mafft-nwnsi"/>
@@ -58,31 +63,32 @@
             <when value="mafft-linsi"/>
             <when value="mafft-qinsi"/>
             <when value="mafft-xinsi"/>
-            <when value="custom"/>
         </conditional>
-        <conditional name="cond_outformat">
-            <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
-                <option value="fasta" selected="true">FASTA</option>
-                <option value="clustalw">ClustalW</option>
-            </param>
-            <when value="fasta"/>
-            <when value="clustalw"/>
-        </conditional>
+        <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
+            <option value="fasta" selected="true">FASTA</option>
+            <option value="clustalw">ClustalW</option>
+        </param>
     </inputs>
     <outputs>
         <data format="fasta" name="outputFasta" label="${tool.name} on ${on_string}">
-            <filter>(cond_outformat['outputFormat'] == 'fasta')</filter>
+            <filter>outputFormat == 'fasta'</filter>
         </data>
         <data format="clustal" name="outputClustalW" label="${tool.name} on ${on_string}">
-            <filter>(cond_outformat['outputFormat'] == 'clustalw')</filter>
+            <filter>outputFormat == 'clustalw'</filter>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="inputSequences" value="sample"/>
-            <param name="flavourType" value="fftns"/>
+            <param name="inputSequences" value="sample.fa"/>
+            <param name="flavourType" value="mafft-fftns"/>
             <param name="outputFormat" value="fasta"/>
-            <output name="outputFasta" file="sample.fftns2"/>
+            <output name="outputFasta" ftype="fasta" file="mafft_fftns_result.aln"/>
+        </test>
+        <test>
+            <param name="inputSequences" value="sample.fa"/>
+            <param name="flavourType" value="mafft-nwns"/>
+            <param name="outputFormat" value="clustalw"/>
+            <output name="outputClustalW" ftype="clustal" file="mafft_nwns_result.aln"/>
         </test>
     </tests>
     <help>
@@ -139,19 +145,14 @@
 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
 
     - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
-    
+
+**Options:**
+
+--auto
+    Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
     ]]>
     </help>
     <citations>
         <citation type="doi">10.1093/molbev/mst010</citation>
-        <citation type="doi">10.1093/nar/gkt389</citation>
-        <citation type="doi">10.1093/bioinformatics/bts578</citation>
-        <citation type="doi">10.1093/bioinformatics/btq224</citation>
-        <citation type="doi">10.1007/978-1-59745-251-9_3</citation>
-        <citation type="doi">10.1186/1471-2105-9-212</citation>
-        <citation type="doi">10.1093/bib/bbn013</citation>
-        <citation type="doi">10.1093/bioinformatics/btl592</citation>
-        <citation type="doi">10.1093/nar/gki198</citation>
-        <citation type="doi">10.1093/nar/gkf436</citation>
     </citations>
 </tool>
diff -r 8817d3a35fac -r 95526e9e3808 test-data/mafft_fftns_result.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mafft_fftns_result.aln	Fri Jul 31 19:00:37 2015 -0400
@@ -0,0 +1,504 @@
+>     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+-------------------MNGTE------------------------GDNF--------
+YVP----F-SNKTGLARSPY----------------EYPQY-------YLAEPWK-----
+----YSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-F
+TVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FR
+FGNTHAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNN
+ESYVVYMFVVHFLVPFVIIFFCYGRLLCTV----KE------------------------
+---------------------------------------------------AAAAQQ---
+------------------------------------------------------------
+--------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-
+HQGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC---------GKN
+PLGD-DE--SGASTSKTEVSSVS-TSPV--------------------------------
+--------------------------------------------SPA-------------
+------
+>     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+-------------------MNGTE------------------------GPNF--------
+YVP----F-SNITGVVRSPF----------------EQPQY-------YLAEPWQ-----
+----FSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-F
+TTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FR
+FGENHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNN
+ESFVIYMFVVHFTIPMIVIFFCYGQLVFTV----KE------------------------
+---------------------------------------------------AAAQQQ---
+------------------------------------------------------------
+--------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-
+HQGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC---------GKN
+PLGD-DE--ASATASKTE------TSQV--------------------------------
+--------------------------------------------APA-------------
+------
+>     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+-------------------MNGTE------------------------GINF--------
+YVP----M-SNKTGVVRSPF----------------EYPQY-------YLAEPWK-----
+----YRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-F
+TVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FR
+FSATHAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHN
+ESYVLYMFVIHFIIPVVVIFFSYGRLICKV----RE------------------------
+---------------------------------------------------AAAQQQ---
+------------------------------------------------------------
+--------------ESATTQK------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT-
+NKGA--DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICC---------GKN
+PFGD-EDVSSTVSQSKTEVSSVS-SSQV--------------------------------
+--------------------------------------------SPA-------------
+------
+>     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+-------------------MNGTE------------------------GKNF--------
+YVP----M-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----
+----FKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-F
+TVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FK
+FSSSHAFAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNN
+ESYVIYMFVCHFILPVAVIFFTYGRLVCTV----KA------------------------
+---------------------------------------------------AAAQQQ---
+------------------------------------------------------------
+--------------DSASTQK------AEREVTKMVILMVFGFLIAWTPYATVAAWIFF-
+NKGA--DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFC---------GKN
+PLGD-DE-SSTVSTSKTEVSS------V--------------------------------
+--------------------------------------------SPA-------------
+------
+>     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+-------------------MNGTE------------------------GNNF--------
+YVP----L-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----
+----FKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-F
+TVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FK
+FSSTHASAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNN
+ESYVLYMFICHFILPVTIIFFTYGRLVCTV----KA------------------------
+---------------------------------------------------AAAQQQ---
+------------------------------------------------------------
+--------------DSASTQK------AEREVTKMVILMVLGFLVAWTPYATVAAWIFF-
+NKGA--AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFC---------GKN
+PLGD-EE-SSTVSTSKTEVSS------V--------------------------------
+--------------------------------------------SPA-------------
+------
+>     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+-------------------MKQVPEF----------------------HEDF--------
+YIPIPLDI-NNLS--AYSPF----------------LVPQD-------HLGNQGI-----
+----FMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-S
+PLSFYSFFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-FT
+FKTPHAIAGCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSCGPDWYTTNNKYNN
+ESYVMFLFCFCFAVPFGTIVFCYGQLLITL----KL------------------------
+---------------------------------------------------AAKAQA---
+------------------------------------------------------------
+--------------DSASTQK------AEREVTKMVVVMVLGFLVCWAPYASFSLWIVS-
+HRGE--EFDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMM-KMVC---------GKN
+-IEE-DE--ASTSSQVTQVSS------V--------------------------------
+--------------------------------------------APEK------------
+------
+>     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
+-------------------MRKMS------------------------EEEF--------
+YL-----F-KNIS--SVGPW----------------DGPQY-------HIAPVWA-----
+----FYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-V
+FPVFVASCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-FR
+FSSKHALTVVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSCGPDWYTVGTKYRS
+ESYTWFLFIFCFIVPLSLICFSYTQLLRAL----KA------------------------
+---------------------------------------------------VAAQQQ---
+------------------------------------------------------------
+--------------ESATTQK------AEREVSRMVVVMVGSFCVCYVPYAAFAMYMVN-
+NRNH--GLDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIM-KMVC---------GKA
+-MTD-ES--DTCSSQKTEVSTVS-STQV--------------------------------
+--------------------------------------------GPN-------------
+------
+>     8=opsin, greensensitive  human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------------------------------DLAETVIA-S
+TISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VR
+FDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
+QSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RA------------------------
+---------------------------------------------------VAKQQK---
+------------------------------------------------------------
+--------------ESESTQK------AEKEVTRMVVVMVLAFC----------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------
+>     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
+-------------------MAQQWSL----------QRLAGRHPQDSYEDST--------
+QSSI-FTY-TNSNS-TRGPF----------------EGPNY-------HIAPRWV-----
+----YHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-S
+TISVVNQVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-VR
+FDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
+QSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RA------------------------
+---------------------------------------------------VAKQQK---
+------------------------------------------------------------
+--------------ESESTQK------AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAA-
+NPGY--PFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCIL-QLF----------GKK
+-VDD-GS--ELSSASKTEVSSV---SSV--------------------------------
+--------------------------------------------SPA-------------
+------
+>    10== Z68193   1 human Red Opsin <>[]
+-------------------MAQQWSL----------QRLAGRHPQDSYEDST--------
+QSSI-FTY-TNSNS-TRGPF----------------EGPNY-------HIAPRWV-----
+----YHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-S
+TISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VR
+FDAKLAIVGIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
+QSYMIVLMVTCCIIPLAIIMLCYLQVWLAI----RA------------------------
+---------------------------------------------------VAKQQK---
+------------------------------------------------------------
+--------------ESESTQK------AEKEVTRMVVVMIFAYCVCWGPYTFFACFAAA-
+NPGY--AFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCIL-QLF----------GKK
+-VDD-GS--ELSSASKTEVSSV---SSV--------------------------------
+--------------------------------------------SPA-------------
+------
+>    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+-------------------MTEAWNV----------AVFAARRSRDD-DDTT--------
+RGSV-FTY-TNTNN-TRGPF----------------EGPNY-------HIAPRWV-----
+----YNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-S
+TISVFNQIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-IK
+FDSKLAIIGIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSVELGC
+QSFMLTLMITCCFLPLFIIIVCYLQVWMAI----RA------------------------
+---------------------------------------------------VAAQQK---
+------------------------------------------------------------
+--------------ESESTQK------AEREVSRMVVVMIVAFCICWGPYASFVSFAAA-
+NPGY--AFHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIM-QLF----------GKK
+-VDD-GS--EASTTSRTEVSSVS-NSSV--------------------------------
+--------------------------------------------APA-------------
+------
+>    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
+-------------------MA-AWEA----------AFAARRRHEE--EDTT--------
+RDSV-FTY-TNSNN-TRGPF----------------EGPNY-------HIAPRWV-----
+----YNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-S
+TISVINQIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-IK
+FDGKLAVAGILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSDPGV
+QSYMVVLMVTCCFFPLAIIILCYLQVWLAI----RA------------------------
+---------------------------------------------------VAAQQK---
+------------------------------------------------------------
+--------------ESESTQK------AEKEVSRMVVVMIVAYCFCWGPYTFFACFAAA-
+NPGY--AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIL-QLF----------GKK
+-VDD-GS--EVST-SRTEVSSVS-NSSV--------------------------------
+--------------------------------------------SPA-------------
+------
+>    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+-------------------MS---------------------------SNSS--------
+QAP--------PNG-TPGPF----------------DGPQW------PYQAPQST-----
+----YVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-S
+SVSLSNNIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-FQ
+FQRRHAVSGCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSCGPNWYTGGSNN--
+NSYILSLFVTCFVLPLSLILFSYTNLLLTL----RA------------------------
+---------------------------------------------------AAAQQK---
+------------------------------------------------------------
+--------------EADTTQR------AEREVTRMVIVMVMAFLLCWLPYSTFALVVAT-
+HKGI--IIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLL-EMLCCGY-----QPQR
+-TGK-AS--PGTPGPHADVTAAGLRNKV--------------------------------
+--------------------------------------------MPAHP---V-------
+------
+>    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+----------MESGNVSSSLFGNVST----------ALRPEARL----SA----------
+-ETRLLGW--------NVPP----------------EELR--------HIPEHWLTYPEP
+PESMNYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--T
+PIFIYNSFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--K
+MTHGKAIAMIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSCTFDYLT--DNFDT
+RLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA------------------------
+---------------------------------------------------LRDQAKKM-
+--------------------------------NVESL-----------------------
+-----------RSNVDKNKET------AEIRIAKAAITICFLFFCSWTPYGVMSLIGAF-
+GDKT--LLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLAL--------N
+EKAP-ES-SAVASTSTTQEP-QQ-TTAA--------------------------------
+------------------------------------------------------------
+------
+>    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+----------MEYHNVSSVL-GNVSS----------VLRPDARL----SA----------
+-ESRLLGW--------NVPP----------------DELR--------HIPEHWLIYPEP
+PESMNYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--T
+PIFIYNSFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--K
+MTHGKAIAMIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSCTFDYLT--DNFDT
+RLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA------------------------
+---------------------------------------------------LRDQAKKM-
+--------------------------------NVDSL-----------------------
+-----------RSNVDKSKEA------AEIRIAKAAITICFLFFASWTPYGVMSLIGAF-
+GDKT--LLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAI--------S
+EKAP-ES-RAAISTSTTQEQ-QQ-TTAA--------------------------------
+------------------------------------------------------------
+------
+>    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+----------ME------PLCNASEP----------PLRPEAR-----SSGN--------
+GDLQFLGW--------NVPP----------------DQIQ--------YIPEHWLTQLEP
+PASMHYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--A
+PIF--NSFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--N
+MTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDT
+RLFVGTIFFFSFVCPTLMILYYYSQIVGHVFSHEKA------------------------
+---------------------------------------------------LREQAKKM-
+--------------------------------NVESL-----------------------
+-----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-
+GDKS--LLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGV--------N
+EKSG-EI-SSAQST-TTQEQ-QQ-TTAA--------------------------------
+------------------------------------------------------------
+------
+>    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+----------MD------ALCNASEP----------PLRPEARM----SSGS--------
+DELQFLGW--------NVPP----------------DQIQ--------YIPEHWLTQLEP
+PASMHYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--A
+PIFIYNSFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--N
+MTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDT
+RLFVGTIFLFSFVVPTLMILYYYSQIVGHVFNHEKA------------------------
+---------------------------------------------------LREQAKKM-
+--------------------------------NVESL-----------------------
+-----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-
+GDKS--LLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGV--------N
+EKSG-EA-SSAQST-TTQEQTQQ-TSAA--------------------------------
+------------------------------------------------------------
+------
+>    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+-------------------MTNATGP----------QMAYYGAA----SMD---------
+-----FGYPEGVSIVDFVRP----------------EIKP--------YVHQHWYNYPPV
+NPMWHYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-V
+PFFTYNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-PK
+LTTGKAVVFALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSCSYDYLT--QDFNT
+FSYNIFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAA------------------------
+---------------------------------------------------MRAQAKKM-
+--------------------------------NVSTL-----------------------
+-----------RS-NEADAQR------AEIRIAKTALVNVSLWFICWTPYALISLKGVM-
+GDTS--GITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCV------HET
+ETKS-ND-DSQSNSTVAQDKA---------------------------------------
+------------------------------------------------------------
+------
+>    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+-------------------MANVTGP----------QMAFYGSG----AAT---------
+-----FGYPEGMTVADFVPD----------------RVKH--------MVLDHWYNYPPV
+NPMWHYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-F
+PPFCYNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-PK
+LTQGKATFMCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSCSYDYFT--RDMNT
+ITYNICIFIFDFFLPASVIVFSYVFIVKAIFAHEAA------------------------
+---------------------------------------------------MRAQAKKM-
+--------------------------------NVTNL-----------------------
+-----------RS-NEAETQR------AEIRIAKTALVNVSLWFICWTPYAAITIQGLL-
+GNAE--GITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCV------HEK
+DPND-VE-ENQSSNTQTQEKS---------------------------------------
+------------------------------------------------------------
+------
+>    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
+----------ME---SFAVAAAQLGP----------HFAPLS------------------
+----------NGSVVDKVTP----------------DMAH--------LISPYWNQFPAM
+DPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
+MTIPLALGKM---------------------------YVPEGNLTSCGIDYLE--RDWNP
+RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
+---------------------------------------------------MREQAKKM-
+--------------------------------NVKSL-----------------------
+-----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-
+KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
+DDGK-SS-DAQSQATASEAESKA-------------------------------------
+------------------------------------------------------------
+------
+>    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
+----------ME---SFAVAAAQLGP----------HFAPLS------------------
+----------NGSVVDKVTP----------------DMAH--------LISPYWNQFPAM
+DPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
+MTIPLALGKIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSCGIDYLE--RDWNP
+RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
+---------------------------------------------------MREQAKKM-
+--------------------------------NVKSL-----------------------
+-----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-
+KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
+DDGK-SS-DAQSQATASEAESKA-------------------------------------
+------------------------------------------------------------
+------
+>    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+----------MD---SFAAVATQLGP----------QFAAPS------------------
+----------NGSVVDKVTP----------------DMAH--------LISPYWDQFPAM
+DPIWAKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
+MTIPLALGKIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSCGIDYLE--RDWNP
+RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
+---------------------------------------------------MREQAKKM-
+--------------------------------NVKSL-----------------------
+-----------RS-SEDADKS------AEGKLAKVALVTISLWFMAWTPYLVINCMGLF-
+KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
+DDGK-SS-EAQSQATTSEAESKA-------------------------------------
+------------------------------------------------------------
+------
+>    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+-----MERSHLP---ETPFDLAHSGP----------RFQAQSSG----------------
+----------NGSVLDNVLP----------------DMAH--------LVNPYWSRFAPM
+DPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-S
+PVMIINFYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-TP
+MTIKTSIMKILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTACSIDYMT--RMWNP
+RSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKA------------------------
+---------------------------------------------------MREQAKKM-
+--------------------------------NVKSL-----------------------
+-----------RS-SEDCDKS------AEGKLAKVALTTISLWFMAWTPYLVICYFGLF-
+KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVF------GNT
+DEPKPDA-PASDTETTSEADSKA-------------------------------------
+------------------------------------------------------------
+------
+>    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+-----MERSLLP---EPPLAMALLGP----------RFEAQTGG----------------
+----------NRSVLDNVLP----------------DMAP--------LVNPHWSRFAPM
+DPTMSKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-S
+PVMIINFYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-TP
+MTIKTSIMKIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTACSIDYMT--RQWNP
+RSYLITYSLFVYYTPLFMICYSYWFIIATVAAHEKA------------------------
+---------------------------------------------------MRDQAKKM-
+--------------------------------NVKSL-----------------------
+-----------RS-SEDCDKS------AENKLAKVALTTISLWFMAWTPYLIICYFGLF-
+KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVC------GTT
+DEPKPDA-PPSDTETTSEAESKD-------------------------------------
+------------------------------------------------------------
+------
+>    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
+-------------------MIAVSGP----------SYEAFSYG----GQA---------
+----RF---NNQTVVDKVPP----------------DMLH--------LIDANWYQYPPL
+NPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-S
+PPMVINCYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-KP
+LSINGALIRIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTACGTDYFN--RGLLS
+ASYLVCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKN------------------------
+---------------------------------------------------MREQAKKM-
+--------------------------------NVASL-----------------------
+-----------RS-SENQNTS------AECKLAKVALMTISLWFMAWTPYLVINFSGIF-
+NL-V--KISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLAC-------AA
+EPSS-DA-VSTTSGTTTVTDNEK-SNA---------------------------------
+------------------------------------------------------------
+------
+>    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+---------------------MANQL----------SYSSLGWP----YQP---------
+----------NASVVDTMPK----------------EMLY--------MIHEHWYAFPPM
+NPLWYSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-M
+PTMTSNCFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-AP
+LTHKKATLLLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSCTVDYLT--KDWSS
+ASYVVIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQ------------------------
+---------------------------------------------------LREQAKKM-
+--------------------------------NVASL-----------------------
+-----------RANADQQKQS------AECRLAKVAMMTVGLWFMAWTPYLIISWAGVF-
+SSGT--RLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLAC------GSG
+ESGS-DV-KSEASATTTMEEKPK-IPEA--------------------------------
+------------------------------------------------------------
+------
+>    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+------------------------------------MVESTTLV----NQT---------
+-----WWY--NPTVD----------------------------------IHPHWAKFDPI
+PDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGF
+PLKTISAFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKK
+MSHRRAFLMIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSCSFDYLS--TDPST
+RSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKE------------------------
+---------------------------------------------------MAAMAKRL-
+--------------------------------NAKEL-----------------------
+-----------R--KAQAGAS------AEMKLAKISMVIITQFMLSWSPYAIIALLAQF-
+GPAE--WVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKEC
+EDAN-DA-EEEVVASER--GGES-RDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PP
+QGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQG---VDNQAYQA
+------
+>    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+-------------------------------------MGRDLRD----NET---------
+-----WWY--NPSIV----------------------------------VHPHWREFDQV
+PDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGF
+PLMTISCFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKK
+MSHRRAFIMIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNCSFDYIS--RDSTT
+RSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKE------------------------
+---------------------------------------------------MAAMAKRL-
+--------------------------------NAKEL-----------------------
+-----------R--KAQAGAN------AEMRLAKISIVIVSQFLLSWSPYAVVALLAQF-
+GPLE--WVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKET
+EDDK-DA-ETEIPAGESSDAAPS-ADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPP
+QGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQG---VDNQAYQA
+------
+>    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+---------MMD-------VNSSGRPDLYGHLRSF-LLPEVGRGLPDLSPDGGADPVAGS
+WAPHLLS---EVTASPAPTW----------------DAPPDNASGCGEQIN--------Y
+GRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-M
+PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
+QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
+-GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
+----------------------------------P--------GFPR----VEPDS----
+---VIAL-----------------NGIVKLQ--------KEVEECAN-------------
+-----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
+CGTSCSCIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR---------
+-----NINRKLSAAGMHEALKLA-------------------------------------
+-------------------------------------------ERPERPEFVLQNADYCR
+KKGHDS
+>    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+------------------------------------------------------------
+-MPHLLSGFLEVTASPAPTW----------------DAPPDNVSGCGEQIN--------Y
+GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-M
+PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
+QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
+-GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
+----------------------------------P--------GFPR----VQPES----
+---VISL-----------------NGVVKLQ--------KEVEECAN-------------
+-----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
+CGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQCQYR---------
+-----NINRKLSAAGMHEALKLA-------------------------------------
+-------------------------------------------ERPERSEFVLQNSDHCG
+KKGHDT
+>    31=p A47425 serotonin receptor 5HT-7 - rat
+------------------------------------------------------------
+-MPHLLSGFLEVTASPAPTW----------------DAPPDNVSGCGEQIN--------Y
+GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-M
+PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
+QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
+-GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
+----------------------------------P--------GFPR----VQPES----
+---VISL-----------------NGVVKLQ--------KEVEECAN-------------
+-----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
+CGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR---------
+-----NINRKLSAAGMHEALKLA-------------------------------------
+-------------------------------------------ERPERSEFVLQNSDHCG
+KKGHDT
+>    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+----------MD-------VLSPG------------QGNNTTSPPAPFETGG--------
+----------NTTGISDVTV----------------------------------------
+--SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L
+PMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK
+RTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH---------
+-GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------
+---------------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR-
+--------NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAG-
+-PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-
+CESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------
+-----RQ-----------------------------------------------------
+------------------------------------------------------------
+------
+>    33=p A35181 serotonin receptor class 1A - rat
+----------MD-------VFSFG------------QGNNTTASQEPFGTGG--------
+----------NVTSISDVTF----------------------------------------
+--SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L
+PMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK
+RTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH---------
+-GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------
+---------------TVRKVEKKGAGTSLGTSSAPPPKKS-----------LNGQPGSG-
+--------DWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESG-
+-SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-
+CESSC-HMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------
+-----RR-----------------------------------------------------
+------------------------------------------------------------
+------
+>    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALD-------VARMG-----GLASTPSGLRSTGLTTPGLSPTG--------
+----------LVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVY
+SHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-M
+PLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRR
+RSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK---------
+-GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTE
+YSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS--
+--------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS-
+------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-
+VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------
+-----RGHR---------------------------------------------------
+------------------------------------------------------------
+------
+>    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALD-------VARMG-----GLASTPSGLRSTGLTTPGLSPTG--------
+----------LVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVY
+SHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-M
+PLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRR
+RSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK---------
+-GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTE
+YSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS--
+--------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS-
+------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-
+VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------
+-----RGHR---------------------------------------------------
+------------------------------------------------------------
+------
+>    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+-MEGAEGQEELD-------WEAL-------YLRLP--LQNCSWNSTGWEPNW--------
+----------NVTVVPNTTW---------WQASAPFDTPAALVRAAAK------------
+--------AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-M
+PLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHA
+STAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV---------
+-GYQIFATASSFYVPVLIILILYWRIYQTARKRIR-------------------------
+--------------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGI
+AAAVVAVIGRPLPTISETTTTGFTNVSS----NNTS---PEKQSCANGLEADPPTTGYGA
+VAAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-
+CDCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRV---------
+-----RRRRA--------------------------------------------------
+---------------------------------------------PQ-------------
+------
diff -r 8817d3a35fac -r 95526e9e3808 test-data/mafft_nwns_result.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mafft_nwns_result.aln	Fri Jul 31 19:00:37 2015 -0400
@@ -0,0 +1,496 @@
+CLUSTAL format alignment by MAFFT NW-NS-2 (v7.221)
+
+
+1==             -------------------MNGTE------------------------GDNF--------
+2==             -------------------MNGTE------------------------GPNF--------
+3==             -------------------MNGTE------------------------GINF--------
+4=p             -------------------MNGTE------------------------GKNF--------
+5=p             -------------------MNGTE------------------------GNNF--------
+6==             -------------------MKQVPEF----------------------HEDF--------
+7==             -------------------MRKMS------------------------EEEF--------
+8=opsin,        ------------------------------------------------------------
+9==             -------------------MAQQWSL----------QRLAGRHPQDSYEDST--------
+10==            -------------------MAQQWSL----------QRLAGRHPQDSYEDST--------
+11==            -------------------MTEAWNV----------AVFAARRSRDD-DDTT--------
+12==            -------------------MA-AWEA----------AFAARRRHEE--EDTT--------
+13==            -------------------MS---------------------------SNSS--------
+14==            ----------MESGNVSSSLFGNVST----------ALRPEARL----SA----------
+15==            ----------MEYHNVSSVL-GNVSS----------VLRPDARL----SA----------
+16==            ----------ME------PLCNASEP----------PLRPEAR-----SSGN--------
+17==            ----------MD------ALCNASEP----------PLRPEARM----SSGS--------
+18==            -------------------MTNATGP----------QMAYYGAA----SMD---------
+19==            -------------------MANVTGP----------QMAFYGSG----AAT---------
+20==            ----------ME---SFAVAAAQLGP----------HFAPLS------------------
+21==            ----------ME---SFAVAAAQLGP----------HFAPLS------------------
+22==            ----------MD---SFAAVATQLGP----------QFAAPS------------------
+23==            -----MERSHLP---ETPFDLAHSGP----------RFQAQSSG----------------
+24==            -----MERSLLP---EPPLAMALLGP----------RFEAQTGG----------------
+25==            -------------------MIAVSGP----------SYEAFSYG----GQA---------
+26==            ---------------------MANQL----------SYSSLGWP----YQP---------
+27==            ------------------------------------MVESTTLV----NQT---------
+28==            -------------------------------------MGRDLRD----NET---------
+29==            ---------MMD-------VNSSGRPDLYGHLRSF-LLPEVGRGLPDLSPDGGADPVAGS
+30==            ------------------------------------------------------------
+31=p            ------------------------------------------------------------
+32==            ----------MD-------VLSPG------------QGNNTTSPPAPFETGG--------
+33=p            ----------MD-------VFSFG------------QGNNTTASQEPFGTGG--------
+34==            MANFTFGDLALD-------VARMG-----GLASTPSGLRSTGLTTPGLSPTG--------
+35=p            MANFTFGDLALD-------VARMG-----GLASTPSGLRSTGLTTPGLSPTG--------
+36==            -MEGAEGQEELD-------WEAL-------YLRLP--LQNCSWNSTGWEPNW--------
+                                                                            
+
+1==             YVP----F-SNKTGLARSPY----------------EYPQY-------YLAEPWK-----
+2==             YVP----F-SNITGVVRSPF----------------EQPQY-------YLAEPWQ-----
+3==             YVP----M-SNKTGVVRSPF----------------EYPQY-------YLAEPWK-----
+4=p             YVP----M-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----
+5=p             YVP----L-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----
+6==             YIPIPLDI-NNLS--AYSPF----------------LVPQD-------HLGNQGI-----
+7==             YL-----F-KNIS--SVGPW----------------DGPQY-------HIAPVWA-----
+8=opsin,        ------------------------------------------------------------
+9==             QSSI-FTY-TNSNS-TRGPF----------------EGPNY-------HIAPRWV-----
+10==            QSSI-FTY-TNSNS-TRGPF----------------EGPNY-------HIAPRWV-----
+11==            RGSV-FTY-TNTNN-TRGPF----------------EGPNY-------HIAPRWV-----
+12==            RDSV-FTY-TNSNN-TRGPF----------------EGPNY-------HIAPRWV-----
+13==            QAP--------PNG-TPGPF----------------DGPQW------PYQAPQST-----
+14==            -ETRLLGW--------NVPP----------------EELR--------HIPEHWLTYPEP
+15==            -ESRLLGW--------NVPP----------------DELR--------HIPEHWLIYPEP
+16==            GDLQFLGW--------NVPP----------------DQIQ--------YIPEHWLTQLEP
+17==            DELQFLGW--------NVPP----------------DQIQ--------YIPEHWLTQLEP
+18==            -----FGYPEGVSIVDFVRP----------------EIKP--------YVHQHWYNYPPV
+19==            -----FGYPEGMTVADFVPD----------------RVKH--------MVLDHWYNYPPV
+20==            ----------NGSVVDKVTP----------------DMAH--------LISPYWNQFPAM
+21==            ----------NGSVVDKVTP----------------DMAH--------LISPYWNQFPAM
+22==            ----------NGSVVDKVTP----------------DMAH--------LISPYWDQFPAM
+23==            ----------NGSVLDNVLP----------------DMAH--------LVNPYWSRFAPM
+24==            ----------NRSVLDNVLP----------------DMAP--------LVNPHWSRFAPM
+25==            ----RF---NNQTVVDKVPP----------------DMLH--------LIDANWYQYPPL
+26==            ----------NASVVDTMPK----------------EMLY--------MIHEHWYAFPPM
+27==            -----WWY--NPTVD----------------------------------IHPHWAKFDPI
+28==            -----WWY--NPSIV----------------------------------VHPHWREFDQV
+29==            WAPHLLS---EVTASPAPTW----------------DAPPDNASGCGEQIN--------Y
+30==            -MPHLLSGFLEVTASPAPTW----------------DAPPDNVSGCGEQIN--------Y
+31=p            -MPHLLSGFLEVTASPAPTW----------------DAPPDNVSGCGEQIN--------Y
+32==            ----------NTTGISDVTV----------------------------------------
+33=p            ----------NVTSISDVTF----------------------------------------
+34==            ----------LVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVY
+35=p            ----------LVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVY
+36==            ----------NVTVVPNTTW---------WQASAPFDTPAALVRAAAK------------
+                                                                            
+
+1==             ----YSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-F
+2==             ----FSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-F
+3==             ----YRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-F
+4=p             ----FKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-F
+5=p             ----FKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-F
+6==             ----FMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-S
+7==             ----FYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-V
+8=opsin,        --------------------------------------------------DLAETVIA-S
+9==             ----YHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-S
+10==            ----YHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-S
+11==            ----YNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-S
+12==            ----YNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-S
+13==            ----YVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-S
+14==            PESMNYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--T
+15==            PESMNYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--T
+16==            PASMHYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--A
+17==            PASMHYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--A
+18==            NPMWHYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-V
+19==            NPMWHYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-F
+20==            DPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+21==            DPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+22==            DPIWAKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+23==            DPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-S
+24==            DPTMSKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-S
+25==            NPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-S
+26==            NPLWYSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-M
+27==            PDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGF
+28==            PDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGF
+29==            GRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-M
+30==            GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-M
+31=p            GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-M
+32==            --SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L
+33=p            --SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L
+34==            SHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-M
+35=p            SHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-M
+36==            --------AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-M
+                                                                  .         
+
+1==             TVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FR
+2==             TTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FR
+3==             TVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FR
+4=p             TVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FK
+5=p             TVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FK
+6==             PLSFYSFFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-FT
+7==             FPVFVASCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-FR
+8=opsin,        TISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VR
+9==             TISVVNQVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-VR
+10==            TISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VR
+11==            TISVFNQIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-IK
+12==            TISVINQIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-IK
+13==            SVSLSNNIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-FQ
+14==            PIFIYNSFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--K
+15==            PIFIYNSFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--K
+16==            PIF--NSFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--N
+17==            PIFIYNSFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--N
+18==            PFFTYNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-PK
+19==            PPFCYNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-PK
+20==            PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
+21==            PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
+22==            PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
+23==            PVMIINFYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-TP
+24==            PVMIINFYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-TP
+25==            PPMVINCYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-KP
+26==            PTMTSNCFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-AP
+27==            PLKTISAFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKK
+28==            PLMTISCFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKK
+29==            PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
+30==            PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
+31=p            PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
+32==            PMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK
+33=p            PMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK
+34==            PLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRR
+35=p            PLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRR
+36==            PLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHA
+                            :   :    * :                  :  :*:  :   :     
+
+1==             FGNTHAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNN
+2==             FGENHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNN
+3==             FSATHAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHN
+4=p             FSSSHAFAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNN
+5=p             FSSTHASAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNN
+6==             FKTPHAIAGCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSCGPDWYTTNNKYNN
+7==             FSSKHALTVVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSCGPDWYTVGTKYRS
+8=opsin,        FDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
+9==             FDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
+10==            FDAKLAIVGIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
+11==            FDSKLAIIGIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSVELGC
+12==            FDGKLAVAGILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSDPGV
+13==            FQRRHAVSGCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSCGPNWYTGGSNN--
+14==            MTHGKAIAMIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSCTFDYLT--DNFDT
+15==            MTHGKAIAMIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSCTFDYLT--DNFDT
+16==            MTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDT
+17==            MTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDT
+18==            LTTGKAVVFALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSCSYDYLT--QDFNT
+19==            LTQGKATFMCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSCSYDYFT--RDMNT
+20==            MTIPLALGKM---------------------------YVPEGNLTSCGIDYLE--RDWNP
+21==            MTIPLALGKIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSCGIDYLE--RDWNP
+22==            MTIPLALGKIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSCGIDYLE--RDWNP
+23==            MTIKTSIMKILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTACSIDYMT--RMWNP
+24==            MTIKTSIMKIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTACSIDYMT--RQWNP
+25==            LSINGALIRIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTACGTDYFN--RGLLS
+26==            LTHKKATLLLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSCTVDYLT--KDWSS
+27==            MSHRRAFLMIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSCSFDYLS--TDPST
+28==            MSHRRAFIMIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNCSFDYIS--RDSTT
+29==            QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
+30==            QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
+31=p            QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
+32==            RTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH---------
+33=p            RTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH---------
+34==            RSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK---------
+35=p            RSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK---------
+36==            STAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV---------
+                                                                 :          
+
+1==             ESYVVYMFVVHFLVPFVIIFFCYGRLLCTV----KE------------------------
+2==             ESFVIYMFVVHFTIPMIVIFFCYGQLVFTV----KE------------------------
+3==             ESYVLYMFVIHFIIPVVVIFFSYGRLICKV----RE------------------------
+4=p             ESYVIYMFVCHFILPVAVIFFTYGRLVCTV----KA------------------------
+5=p             ESYVLYMFICHFILPVTIIFFTYGRLVCTV----KA------------------------
+6==             ESYVMFLFCFCFAVPFGTIVFCYGQLLITL----KL------------------------
+7==             ESYTWFLFIFCFIVPLSLICFSYTQLLRAL----KA------------------------
+8=opsin,        QSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RA------------------------
+9==             QSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RA------------------------
+10==            QSYMIVLMVTCCIIPLAIIMLCYLQVWLAI----RA------------------------
+11==            QSFMLTLMITCCFLPLFIIIVCYLQVWMAI----RA------------------------
+12==            QSYMVVLMVTCCFFPLAIIILCYLQVWLAI----RA------------------------
+13==            NSYILSLFVTCFVLPLSLILFSYTNLLLTL----RA------------------------
+14==            RLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA------------------------
+15==            RLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA------------------------
+16==            RLFVGTIFFFSFVCPTLMILYYYSQIVGHVFSHEKA------------------------
+17==            RLFVGTIFLFSFVVPTLMILYYYSQIVGHVFNHEKA------------------------
+18==            FSYNIFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAA------------------------
+19==            ITYNICIFIFDFFLPASVIVFSYVFIVKAIFAHEAA------------------------
+20==            RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
+21==            RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
+22==            RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
+23==            RSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKA------------------------
+24==            RSYLITYSLFVYYTPLFMICYSYWFIIATVAAHEKA------------------------
+25==            ASYLVCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKN------------------------
+26==            ASYVVIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQ------------------------
+27==            RSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKE------------------------
+28==            RSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKE------------------------
+29==            -GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
+30==            -GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
+31=p            -GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
+32==            -GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------
+33=p            -GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------
+34==            -GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTE
+35=p            -GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTE
+36==            -GYQIFATASSFYVPVLIILILYWRIYQTARKRIR-------------------------
+                              *   :   *  :                                  
+
+1==             ---------------------------------------------------AAAAQQ---
+2==             ---------------------------------------------------AAAQQQ---
+3==             ---------------------------------------------------AAAQQQ---
+4=p             ---------------------------------------------------AAAQQQ---
+5=p             ---------------------------------------------------AAAQQQ---
+6==             ---------------------------------------------------AAKAQA---
+7==             ---------------------------------------------------VAAQQQ---
+8=opsin,        ---------------------------------------------------VAKQQK---
+9==             ---------------------------------------------------VAKQQK---
+10==            ---------------------------------------------------VAKQQK---
+11==            ---------------------------------------------------VAAQQK---
+12==            ---------------------------------------------------VAAQQK---
+13==            ---------------------------------------------------AAAQQK---
+14==            ---------------------------------------------------LRDQAKKM-
+15==            ---------------------------------------------------LRDQAKKM-
+16==            ---------------------------------------------------LREQAKKM-
+17==            ---------------------------------------------------LREQAKKM-
+18==            ---------------------------------------------------MRAQAKKM-
+19==            ---------------------------------------------------MRAQAKKM-
+20==            ---------------------------------------------------MREQAKKM-
+21==            ---------------------------------------------------MREQAKKM-
+22==            ---------------------------------------------------MREQAKKM-
+23==            ---------------------------------------------------MREQAKKM-
+24==            ---------------------------------------------------MRDQAKKM-
+25==            ---------------------------------------------------MREQAKKM-
+26==            ---------------------------------------------------LREQAKKM-
+27==            ---------------------------------------------------MAAMAKRL-
+28==            ---------------------------------------------------MAAMAKRL-
+29==            ----------------------------------P--------GFPR----VEPDS----
+30==            ----------------------------------P--------GFPR----VQPES----
+31=p            ----------------------------------P--------GFPR----VQPES----
+32==            ---------------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR-
+33=p            ---------------TVRKVEKKGAGTSLGTSSAPPPKKS-----------LNGQPGSG-
+34==            YSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS--
+35=p            YSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS--
+36==            --------------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGI
+                                                                            
+
+1==             ------------------------------------------------------------
+2==             ------------------------------------------------------------
+3==             ------------------------------------------------------------
+4=p             ------------------------------------------------------------
+5=p             ------------------------------------------------------------
+6==             ------------------------------------------------------------
+7==             ------------------------------------------------------------
+8=opsin,        ------------------------------------------------------------
+9==             ------------------------------------------------------------
+10==            ------------------------------------------------------------
+11==            ------------------------------------------------------------
+12==            ------------------------------------------------------------
+13==            ------------------------------------------------------------
+14==            --------------------------------NVESL-----------------------
+15==            --------------------------------NVDSL-----------------------
+16==            --------------------------------NVESL-----------------------
+17==            --------------------------------NVESL-----------------------
+18==            --------------------------------NVSTL-----------------------
+19==            --------------------------------NVTNL-----------------------
+20==            --------------------------------NVKSL-----------------------
+21==            --------------------------------NVKSL-----------------------
+22==            --------------------------------NVKSL-----------------------
+23==            --------------------------------NVKSL-----------------------
+24==            --------------------------------NVKSL-----------------------
+25==            --------------------------------NVASL-----------------------
+26==            --------------------------------NVASL-----------------------
+27==            --------------------------------NAKEL-----------------------
+28==            --------------------------------NAKEL-----------------------
+29==            ---VIAL-----------------NGIVKLQ--------KEVEECAN-------------
+30==            ---VISL-----------------NGVVKLQ--------KEVEECAN-------------
+31=p            ---VISL-----------------NGVVKLQ--------KEVEECAN-------------
+32==            --------NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAG-
+33=p            --------DWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESG-
+34==            --------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS-
+35=p            --------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS-
+36==            AAAVVAVIGRPLPTISETTTTGFTNVSS----NNTS---PEKQSCANGLEADPPTTGYGA
+                                                                            
+
+1==             --------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-
+2==             --------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-
+3==             --------------ESATTQK------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT-
+4=p             --------------DSASTQK------AEREVTKMVILMVFGFLIAWTPYATVAAWIFF-
+5=p             --------------DSASTQK------AEREVTKMVILMVLGFLVAWTPYATVAAWIFF-
+6==             --------------DSASTQK------AEREVTKMVVVMVLGFLVCWAPYASFSLWIVS-
+7==             --------------ESATTQK------AEREVSRMVVVMVGSFCVCYVPYAAFAMYMVN-
+8=opsin,        --------------ESESTQK------AEKEVTRMVVVMVLAFC----------------
+9==             --------------ESESTQK------AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAA-
+10==            --------------ESESTQK------AEKEVTRMVVVMIFAYCVCWGPYTFFACFAAA-
+11==            --------------ESESTQK------AEREVSRMVVVMIVAFCICWGPYASFVSFAAA-
+12==            --------------ESESTQK------AEKEVSRMVVVMIVAYCFCWGPYTFFACFAAA-
+13==            --------------EADTTQR------AEREVTRMVIVMVMAFLLCWLPYSTFALVVAT-
+14==            -----------RSNVDKNKET------AEIRIAKAAITICFLFFCSWTPYGVMSLIGAF-
+15==            -----------RSNVDKSKEA------AEIRIAKAAITICFLFFASWTPYGVMSLIGAF-
+16==            -----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-
+17==            -----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-
+18==            -----------RS-NEADAQR------AEIRIAKTALVNVSLWFICWTPYALISLKGVM-
+19==            -----------RS-NEAETQR------AEIRIAKTALVNVSLWFICWTPYAAITIQGLL-
+20==            -----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-
+21==            -----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-
+22==            -----------RS-SEDADKS------AEGKLAKVALVTISLWFMAWTPYLVINCMGLF-
+23==            -----------RS-SEDCDKS------AEGKLAKVALTTISLWFMAWTPYLVICYFGLF-
+24==            -----------RS-SEDCDKS------AENKLAKVALTTISLWFMAWTPYLIICYFGLF-
+25==            -----------RS-SENQNTS------AECKLAKVALMTISLWFMAWTPYLVINFSGIF-
+26==            -----------RANADQQKQS------AECRLAKVAMMTVGLWFMAWTPYLIISWAGVF-
+27==            -----------R--KAQAGAS------AEMKLAKISMVIITQFMLSWSPYAIIALLAQF-
+28==            -----------R--KAQAGAN------AEMRLAKISIVIVSQFLLSWSPYAVVALLAQF-
+29==            -----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
+30==            -----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
+31=p            -----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
+32==            -PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-
+33=p            -SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-
+34==            ------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-
+35=p            ------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-
+36==            VAAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-
+                                            * .           :                 
+
+1==             HQGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC---------GKN
+2==             HQGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC---------GKN
+3==             NKGA--DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICC---------GKN
+4=p             NKGA--DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFC---------GKN
+5=p             NKGA--AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFC---------GKN
+6==             HRGE--EFDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMM-KMVC---------GKN
+7==             NRNH--GLDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIM-KMVC---------GKA
+8=opsin,        ------------------------------------------------------------
+9==             NPGY--PFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCIL-QLF----------GKK
+10==            NPGY--AFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCIL-QLF----------GKK
+11==            NPGY--AFHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIM-QLF----------GKK
+12==            NPGY--AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIL-QLF----------GKK
+13==            HKGI--IIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLL-EMLCCGY-----QPQR
+14==            GDKT--LLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLAL--------N
+15==            GDKT--LLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAI--------S
+16==            GDKS--LLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGV--------N
+17==            GDKS--LLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGV--------N
+18==            GDTS--GITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCV------HET
+19==            GNAE--GITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCV------HEK
+20==            KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
+21==            KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
+22==            KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
+23==            KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVF------GNT
+24==            KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVC------GTT
+25==            NL-V--KISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLAC-------AA
+26==            SSGT--RLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLAC------GSG
+27==            GPAE--WVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKEC
+28==            GPLE--WVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKET
+29==            CGTSCSCIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR---------
+30==            CGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQCQYR---------
+31=p            CGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR---------
+32==            CESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------
+33=p            CESSC-HMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------
+34==            VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------
+35=p            VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------
+36==            CDCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRV---------
+                                                                            
+
+1==             PLGD-DE--SGASTSKTEVSSVS-TSPV--------------------------------
+2==             PLGD-DE--ASATASKTE------TSQV--------------------------------
+3==             PFGD-EDVSSTVSQSKTEVSSVS-SSQV--------------------------------
+4=p             PLGD-DE-SSTVSTSKTEVSS------V--------------------------------
+5=p             PLGD-EE-SSTVSTSKTEVSS------V--------------------------------
+6==             -IEE-DE--ASTSSQVTQVSS------V--------------------------------
+7==             -MTD-ES--DTCSSQKTEVSTVS-STQV--------------------------------
+8=opsin,        ------------------------------------------------------------
+9==             -VDD-GS--ELSSASKTEVSSV---SSV--------------------------------
+10==            -VDD-GS--ELSSASKTEVSSV---SSV--------------------------------
+11==            -VDD-GS--EASTTSRTEVSSVS-NSSV--------------------------------
+12==            -VDD-GS--EVST-SRTEVSSVS-NSSV--------------------------------
+13==            -TGK-AS--PGTPGPHADVTAAGLRNKV--------------------------------
+14==            EKAP-ES-SAVASTSTTQEP-QQ-TTAA--------------------------------
+15==            EKAP-ES-RAAISTSTTQEQ-QQ-TTAA--------------------------------
+16==            EKSG-EI-SSAQST-TTQEQ-QQ-TTAA--------------------------------
+17==            EKSG-EA-SSAQST-TTQEQTQQ-TSAA--------------------------------
+18==            ETKS-ND-DSQSNSTVAQDKA---------------------------------------
+19==            DPND-VE-ENQSSNTQTQEKS---------------------------------------
+20==            DDGK-SS-DAQSQATASEAESKA-------------------------------------
+21==            DDGK-SS-DAQSQATASEAESKA-------------------------------------
+22==            DDGK-SS-EAQSQATTSEAESKA-------------------------------------
+23==            DEPKPDA-PASDTETTSEADSKA-------------------------------------
+24==            DEPKPDA-PPSDTETTSEAESKD-------------------------------------
+25==            EPSS-DA-VSTTSGTTTVTDNEK-SNA---------------------------------
+26==            ESGS-DV-KSEASATTTMEEKPK-IPEA--------------------------------
+27==            EDAN-DA-EEEVVASER--GGES-RDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PP
+28==            EDDK-DA-ETEIPAGESSDAAPS-ADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPP
+29==            -----NINRKLSAAGMHEALKLA-------------------------------------
+30==            -----NINRKLSAAGMHEALKLA-------------------------------------
+31=p            -----NINRKLSAAGMHEALKLA-------------------------------------
+32==            -----RQ-----------------------------------------------------
+33=p            -----RR-----------------------------------------------------
+34==            -----RGHR---------------------------------------------------
+35=p            -----RGHR---------------------------------------------------
+36==            -----RRRRA--------------------------------------------------
+                                                                            
+
+1==             --------------------------------------------SPA-------------
+2==             --------------------------------------------APA-------------
+3==             --------------------------------------------SPA-------------
+4=p             --------------------------------------------SPA-------------
+5=p             --------------------------------------------SPA-------------
+6==             --------------------------------------------APEK------------
+7==             --------------------------------------------GPN-------------
+8=opsin,        ------------------------------------------------------------
+9==             --------------------------------------------SPA-------------
+10==            --------------------------------------------SPA-------------
+11==            --------------------------------------------APA-------------
+12==            --------------------------------------------SPA-------------
+13==            --------------------------------------------MPAHP---V-------
+14==            ------------------------------------------------------------
+15==            ------------------------------------------------------------
+16==            ------------------------------------------------------------
+17==            ------------------------------------------------------------
+18==            ------------------------------------------------------------
+19==            ------------------------------------------------------------
+20==            ------------------------------------------------------------
+21==            ------------------------------------------------------------
+22==            ------------------------------------------------------------
+23==            ------------------------------------------------------------
+24==            ------------------------------------------------------------
+25==            ------------------------------------------------------------
+26==            ------------------------------------------------------------
+27==            QGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQG---VDNQAYQA
+28==            QGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQG---VDNQAYQA
+29==            -------------------------------------------ERPERPEFVLQNADYCR
+30==            -------------------------------------------ERPERSEFVLQNSDHCG
+31=p            -------------------------------------------ERPERSEFVLQNSDHCG
+32==            ------------------------------------------------------------
+33=p            ------------------------------------------------------------
+34==            ------------------------------------------------------------
+35=p            ------------------------------------------------------------
+36==            ---------------------------------------------PQ-------------
+                                                                            
+
+1==             ------
+2==             ------
+3==             ------
+4=p             ------
+5=p             ------
+6==             ------
+7==             ------
+8=opsin,        ------
+9==             ------
+10==            ------
+11==            ------
+12==            ------
+13==            ------
+14==            ------
+15==            ------
+16==            ------
+17==            ------
+18==            ------
+19==            ------
+20==            ------
+21==            ------
+22==            ------
+23==            ------
+24==            ------
+25==            ------
+26==            ------
+27==            ------
+28==            ------
+29==            KKGHDS
+30==            KKGHDT
+31=p            KKGHDT
+32==            ------
+33=p            ------
+34==            ------
+35=p            ------
+36==            ------
+                      
diff -r 8817d3a35fac -r 95526e9e3808 test-data/sample
--- a/test-data/sample	Tue Jun 16 10:54:16 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,285 +0,0 @@
->     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
-MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLF
-VTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG
-GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWSRYIP
-EGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQES
-ASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSAL
-YNPVIYILMNKQFRNCMITTLCCGKNPLGDDESGASTSKTEVSSVSTSPVSPA
->     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
-MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
-VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
-GEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
-EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES
-ATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTLPAFFAKTASI
-YNPIIYIMMNKQFRNCMLTSLCCGKNPLGDDEASATASKTETSQVAPA
->     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
-MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLL
-VTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG
-GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWSRYMP
-EGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQES
-ATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSL
-YNPIIYVLMNKQFRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSSQVSPA
->     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
-MNGTEGKNFYVPMSNRTGLVRSPFEYPQYYLAEPWQFKILALYLFFLMSMGLPINGLTLV
-VTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAVEGFMATLG
-GEVALWSLVVLAIERYIVVCKPMGSFKFSSSHAFAGIAFTWVMALACAAPPLFGWSRYIP
-EGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDS
-ASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGADFSAKFMAIPAFFSKSSAL
-YNPVIYVLLNKQFRNCMLTTIFCGKNPLGDDESSTVSTSKTEVSSVSPA
->     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
-MNGTEGNNFYVPLSNRTGLVRSPFEYPQYYLAEPWQFKLLAVYMFFLICLGLPINGLTLI
-CTAQHKKLRQPLNFILVNLAVAGAIMVCFGFTVTFYTAINGYFALGPTGCAVEGFMATLG
-GEVALWSLVVLAIERYIVVCKPMGSFKFSSTHASAGIAFTWVMAMACAAPPLVGWSRYIP
-EGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDS
-ASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGAAFSAQFMAIPAFFSKTSAL
-YNPVIYVLLNKQFRSCMLTTLFCGKNPLGDEESSTVSTSKTEVSSVSPA
->     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
-MKQVPEFHEDFYIPIPLDINNLSAYSPFLVPQDHLGNQGIFMAMSVFMFFIFIGGASINI
-LTILCTIQFKKLRSHLNYILVNLSIANLFVAIFGSPLSFYSFFNRYFIFGATACKIEGFL
-ATLGGMVGLWSLAVVAFERWLVICKPLGNFTFKTPHAIAGCILPWISALAASLPPLFGWS
-RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKA
-QADSASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVSHRGEEFDLRMATIPSCLSK
-ASTVYNPVIYVLMNKQFRSCMMKMVCGKNIEEDEASTSSQVTQVSSVAPEK
->     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
-MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL
-RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV
-TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGL
-QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT
-QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP
-IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN
->     8=opsin, greensensitive  human (fragment) S07060
-DLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKP
-FGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQS
-YMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFC
->     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
-MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
-IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV
-LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA
-AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL
-QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH
-PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
-VSPA
->    10== Z68193   1 human Red Opsin <>[]
-MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
-IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFV
-LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWS
-AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYL
-QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGYAFH
-PLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
-VSPA
->    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
-MTEAWNVAVFAARRSRDDDDTTRGSVFTYTNTNNTRGPFEGPNYHIAPRWVYNLVSFFMI
-IVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVASTISVFNQIFGYFIL
-GHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGNIKFDSKLAIIGIVFSWVWAW
-GWSAPPIFGWSRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITCCFLPLFIIIVCYLQ
-VWMAIRAVAAQQKESESTQKAEREVSRMVVVMIVAFCICWGPYASFVSFAAANPGYAFHP
-LAAALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLFGKKVDDGSEASTTSRTEVSSVSNS
-SVAPA
->    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
-MAAWEAAFAARRRHEEEDTTRDSVFTYTNSNNTRGPFEGPNYHIAPRWVYNLTSVWMIFV
-VAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIASTISVINQISGYFILGH
-PMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGNIKFDGKLAVAGILFSWLWSCAW
-TAPPIFGWSRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVW
-LAIRAVAAQQKESESTQKAEKEVSRMVVVMIVAYCFCWGPYTFFACFAAANPGYAFHPLA
-AALPAYFAKSATIYNPIIYVFMNRQFRNCILQLFGKKVDDGSEVSTSRTEVSSVSNSSVS
-PA
->    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
-MSSNSSQAPPNGTPGPFDGPQWPYQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYK
-KLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLTGIVGLW
-SLAILALERYVVVCKPLGDFQFQRRHAVSGCAFTWGWALLWSAPPLLGWSSYVPEGLRTS
-CGPNWYTGGSNNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEADTTQRAER
-EVTRMVIVMVMAFLLCWLPYSTFALVVATHKGIIIQPVLASLPSYFSKTATVYNPIIYVF
-MNKQFQSCLLEMLCCGYQPQRTGKASPGTPGPHADVTAAGLRNKVMPAHPV
->    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
-MESGNVSSSLFGNVSTALRPEARLSAETRLLGWNVPPEELRHIPEHWLTYPEPPESMNYL
-LGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVKTPIFIYNSFH
-QGYALGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEGKMTHGKAIAMIIFIY
-MYATPWVVACYTETWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYY
-YSQIVGHVFSHEKALRDQAKKMNVESLRSNVDKNKETAEIRIAKAAITICFLFFCSWTPY
-GVMSLIGAFGDKTLLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLALNE
-KAPESSAVASTSTTQEPQQTTAA
->    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
-MEYHNVSSVLGNVSSVLRPDARLSAESRLLGWNVPPDELRHIPEHWLIYPEPPESMNYLL
-GTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIKTPIFIYNSFHQ
-GYALGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEGKMTHGKAIAMIIFIYL
-YATPWVVACYTESWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYYY
-SQIVGHVFSHEKALRDQAKKMNVDSLRSNVDKSKEAAEIRIAKAAITICFLFFASWTPYG
-VMSLIGAFGDKTLLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAISEK
-APESRAAISTSTTQEQQQTTAA
->    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
-MEPLCNASEPPLRPEARSSGNGDLQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGVF
-YIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFNSFHRGFAIY
-LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYCT
-PWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFFFSFVCPTLMILYYYSQI
-VGHVFSHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVMS
-LIGAFGDKSLLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGVNEKSGE
-ISSAQSTTTQEQQQTTAA
->    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
-MDALCNASEPPLRPEARMSSGSDELQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGV
-FYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFIYNSFHRGF
-ALGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYC
-TPWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFLFSFVVPTLMILYYYSQ
-IVGHVFNHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVM
-SLIGAFGDKSLLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGVNEKSG
-EASSAQSTTTQEQTQQTSAA
->    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
-MTNATGPQMAYYGAASMDFGYPEGVSIVDFVRPEIKPYVHQHWYNYPPVNPMWHYLLGVI
-YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCFSGGV
-WMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFALISWV
-IAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIVFSYV
-FIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQRAEIRIAKTALVNVSLWFICWTPYALI
-SLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCVHETET
-KSNDDSQSNSTVAQDKA
->    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
-MANVTGPQMAFYGSGAATFGYPEGMTVADFVPDRVKHMVLDHWYNYPPVNPMWHYLLGVV
-YLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTNFPPFCYNCFSGGR
-WMFSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNGPKLTQGKATFMCGLAWV
-ISVGWSLPPFFGWGSYTLEGILDSCSYDYFTRDMNTITYNICIFIFDFFLPASVIVFSYV
-FIVKAIFAHEAAMRAQAKKMNVTNLRSNEAETQRAEIRIAKTALVNVSLWFICWTPYAAI
-TIQGLLGNAEGITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCVHEKDP
-NDVEENQSSNTQTQEKS
->    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
-MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
-GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
-MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKMYVPEGNLTSC
-GIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSL
-RSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLFKFEGLTPLNTIWGACFAKS
-AACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDAQSQATASEAESKA
->    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
-MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
-GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
-MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSSIW
-CLAPAFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAA
-VSAHEKAMREQAKKMNVKSLRSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGL
-FKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDA
-QSQATASEAESKA
->    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
-MDSFAAVATQLGPQFAAPSNGSVVDKVTPDMAHLISPYWDQFPAMDPIWAKILTAYMIII
-GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
-MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSTIW
-CCLAPVFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIA
-AVSAHEKAMREQAKKMNVKSLRSSEDADKSAEGKLAKVALVTISLWFMAWTPYLVINCMG
-LFKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSE
-AQSQATTSEAESKA
->    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
-MERSHLPETPFDLAHSGPRFQAQSSGNGSVLDNVLPDMAHLVNPYWSRFAPMDPMMSKIL
-GLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
-ETWVLGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKILFI
-WMMAVFWTVMPLIGWSAYVPEGNLTACSIDYMTRMWNPRSYLITYSLFVYYTPLFLICYS
-YWFIIAAVAAHEKAMREQAKKMNVKSLRSSEDCDKSAEGKLAKVALTTISLWFMAWTPYL
-VICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVFGNTD
-EPKPDAPASDTETTSEADSKA
->    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
-MERSLLPEPPLAMALLGPRFEAQTGGNRSVLDNVLPDMAPLVNPHWSRFAPMDPTMSKIL
-GLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
-ETWVLGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKIAFI
-WMMAVFWTIMPLIGWSSYVPEGNLTACSIDYMTRQWNPRSYLITYSLFVYYTPLFMICYS
-YWFIIATVAAHEKAMRDQAKKMNVKSLRSSEDCDKSAENKLAKVALTTISLWFMAWTPYL
-IICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVCGTTD
-EPKPDAPPSDTETTSEAESKD
->    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
-MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQYPPLNPMWHGILGFVIG
-MLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCMSPPMVINCYYETWVL
-GPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPLSINGALIRIIAIWLFSL
-GWTIAPMFGWNRYVPEGNMTACGTDYFNRGLLSASYLVCYGIWVYFVPLFLIIYSYWFII
-QAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVALMTISLWFMAWTPYLVINFS
-GIFNLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLACAAEPSSDAV
-STTSGTTTVTDNEKSNA
->    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
-MANQLSYSSLGWPYQPNASVVDTMPKEMLYMIHEHWYAFPPMNPLWYSILGVAMIILGII
-CVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFMMPTMTSNCFAETWILGPFMC
-EVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAAAPLTHKKATLLLLFVWIWSGGWTIL
-PFFGWSRYVPEGNLTSCTVDYLTKDWSSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAE
-HEKQLREQAKKMNVASLRANADQQKQSAECRLAKVAMMTVGLWFMAWTPYLIISWAGVFS
-SGTRLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLACGSGESGSDVKSE
-ASATTTMEEKPKIPEA
->    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
-MVESTTLVNQTWWYNPTVDIHPHWAKFDPIPDAVYYSVGIFIGVVGIIGILGNGVVIYLF
-SKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMKKWIFGKVACQLYGLLGGIFG
-FMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVWSVGPVFNWGAYVP
-EGILTSCSFDYLSTDPSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAK
-RLNAKELRKAQAGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQFGPAEWVTPYAAEL
-PVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECEDANDAEEEVVASER
-GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGYPPQGYPPQGAYPPPQGYPPQGYPP
-QGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
->    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
-MGRDLRDNETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFT
-KTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGF
-MSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLWAIGPIFGWGAYTLE
-GVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKR
-LNAKELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLP
-VMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIPAGESS
-DAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGY
-PPPPQGAPPQGAPPAAPPQGVDNQAYQA
->    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
-MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLSEVTASPAPTW
-DAPPDNASGCGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLI
-VSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAMDVMCCTASIMTLCVISIDR
-YLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGWAQNVNDDKVCLISQDFGYT
-IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDSVIALNGIVKLQKEVE
-ECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC
-IPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALK
-LAERPERPEFVLQNADYCRKKGHDS
->    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
-MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
-VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
-DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
-AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
-QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
-PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQC
-QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
->    31=p A47425 serotonin receptor 5HT-7 - rat
-MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
-VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
-DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
-AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
-QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
-PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQC
-QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
->    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
-MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAA
-IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
-RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT
-RHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGN
-SKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
-FFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
-RQ
->    33=p A35181 serotonin receptor class 1A - rat
-MDVFSFGQGNNTTASQEPFGTGGNVTSISDVTFSYQVITSLLLGTLIFCAVLGNACVVAA
-IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
-RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT
-SLGTSSAPPPKKSLNGQPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGN
-SKEHLPLPSESGSNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
-FFIVALVLPFCESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
-RR
->    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
-MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
-HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
-MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
-ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
-DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
-ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
-NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
-LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
-NPIIYTIFSPEFRSAFQKILFGKYRRGHR
->    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
-MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
-HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
-MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
-ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
-DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
-ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
-NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
-LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
-NPIIYTIFSPEFRSAFQKILFGKYRRGHR
->    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
-MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVVPNTTWWQASAPFDTPAALVR
-AAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLVMPLGAV
-YEVVQRWTLGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTNIDYIHASTAKRVGMM
-IACVWTVSFFVCIAQLLGWKDPDWNQRVSEDLRCVVSQDVGYQIFATASSFYVPVLIILI
-LYWRIYQTARKRIRRRRGATARGGVGPPPVPAGGALVAGGGSGGIAAAVVAVIGRPLPTI
-SETTTTGFTNVSSNNTSPEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKR
-ERKAAKTLAIITGAFVACWLPFFVLAILVPTCDCEVSPVLTSLSLWLGYFNSTLNPVIYT
-VFSPEFRHAFQRLLCGRRVRRRRAPQ
diff -r 8817d3a35fac -r 95526e9e3808 test-data/sample.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample.fa	Fri Jul 31 19:00:37 2015 -0400
@@ -0,0 +1,285 @@
+>     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLF
+VTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG
+GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWSRYIP
+EGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQES
+ASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSAL
+YNPVIYILMNKQFRNCMITTLCCGKNPLGDDESGASTSKTEVSSVSTSPVSPA
+>     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
+VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
+GEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
+EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES
+ATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTLPAFFAKTASI
+YNPIIYIMMNKQFRNCMLTSLCCGKNPLGDDEASATASKTETSQVAPA
+>     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLL
+VTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG
+GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWSRYMP
+EGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQES
+ATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSL
+YNPIIYVLMNKQFRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSSQVSPA
+>     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+MNGTEGKNFYVPMSNRTGLVRSPFEYPQYYLAEPWQFKILALYLFFLMSMGLPINGLTLV
+VTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAVEGFMATLG
+GEVALWSLVVLAIERYIVVCKPMGSFKFSSSHAFAGIAFTWVMALACAAPPLFGWSRYIP
+EGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDS
+ASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGADFSAKFMAIPAFFSKSSAL
+YNPVIYVLLNKQFRNCMLTTIFCGKNPLGDDESSTVSTSKTEVSSVSPA
+>     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+MNGTEGNNFYVPLSNRTGLVRSPFEYPQYYLAEPWQFKLLAVYMFFLICLGLPINGLTLI
+CTAQHKKLRQPLNFILVNLAVAGAIMVCFGFTVTFYTAINGYFALGPTGCAVEGFMATLG
+GEVALWSLVVLAIERYIVVCKPMGSFKFSSTHASAGIAFTWVMAMACAAPPLVGWSRYIP
+EGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDS
+ASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGAAFSAQFMAIPAFFSKTSAL
+YNPVIYVLLNKQFRSCMLTTLFCGKNPLGDEESSTVSTSKTEVSSVSPA
+>     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+MKQVPEFHEDFYIPIPLDINNLSAYSPFLVPQDHLGNQGIFMAMSVFMFFIFIGGASINI
+LTILCTIQFKKLRSHLNYILVNLSIANLFVAIFGSPLSFYSFFNRYFIFGATACKIEGFL
+ATLGGMVGLWSLAVVAFERWLVICKPLGNFTFKTPHAIAGCILPWISALAASLPPLFGWS
+RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKA
+QADSASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVSHRGEEFDLRMATIPSCLSK
+ASTVYNPVIYVLMNKQFRSCMMKMVCGKNIEEDEASTSSQVTQVSSVAPEK
+>     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
+MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL
+RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV
+TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGL
+QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT
+QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP
+IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN
+>     8=opsin, greensensitive  human (fragment) S07060
+DLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKP
+FGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQS
+YMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFC
+>     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
+IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA
+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL
+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH
+PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
+VSPA
+>    10== Z68193   1 human Red Opsin <>[]
+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
+IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFV
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWS
+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYL
+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGYAFH
+PLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
+VSPA
+>    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+MTEAWNVAVFAARRSRDDDDTTRGSVFTYTNTNNTRGPFEGPNYHIAPRWVYNLVSFFMI
+IVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVASTISVFNQIFGYFIL
+GHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGNIKFDSKLAIIGIVFSWVWAW
+GWSAPPIFGWSRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITCCFLPLFIIIVCYLQ
+VWMAIRAVAAQQKESESTQKAEREVSRMVVVMIVAFCICWGPYASFVSFAAANPGYAFHP
+LAAALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLFGKKVDDGSEASTTSRTEVSSVSNS
+SVAPA
+>    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
+MAAWEAAFAARRRHEEEDTTRDSVFTYTNSNNTRGPFEGPNYHIAPRWVYNLTSVWMIFV
+VAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIASTISVINQISGYFILGH
+PMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGNIKFDGKLAVAGILFSWLWSCAW
+TAPPIFGWSRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVW
+LAIRAVAAQQKESESTQKAEKEVSRMVVVMIVAYCFCWGPYTFFACFAAANPGYAFHPLA
+AALPAYFAKSATIYNPIIYVFMNRQFRNCILQLFGKKVDDGSEVSTSRTEVSSVSNSSVS
+PA
+>    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+MSSNSSQAPPNGTPGPFDGPQWPYQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYK
+KLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLTGIVGLW
+SLAILALERYVVVCKPLGDFQFQRRHAVSGCAFTWGWALLWSAPPLLGWSSYVPEGLRTS
+CGPNWYTGGSNNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEADTTQRAER
+EVTRMVIVMVMAFLLCWLPYSTFALVVATHKGIIIQPVLASLPSYFSKTATVYNPIIYVF
+MNKQFQSCLLEMLCCGYQPQRTGKASPGTPGPHADVTAAGLRNKVMPAHPV
+>    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+MESGNVSSSLFGNVSTALRPEARLSAETRLLGWNVPPEELRHIPEHWLTYPEPPESMNYL
+LGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVKTPIFIYNSFH
+QGYALGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEGKMTHGKAIAMIIFIY
+MYATPWVVACYTETWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYY
+YSQIVGHVFSHEKALRDQAKKMNVESLRSNVDKNKETAEIRIAKAAITICFLFFCSWTPY
+GVMSLIGAFGDKTLLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLALNE
+KAPESSAVASTSTTQEPQQTTAA
+>    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+MEYHNVSSVLGNVSSVLRPDARLSAESRLLGWNVPPDELRHIPEHWLIYPEPPESMNYLL
+GTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIKTPIFIYNSFHQ
+GYALGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEGKMTHGKAIAMIIFIYL
+YATPWVVACYTESWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYYY
+SQIVGHVFSHEKALRDQAKKMNVDSLRSNVDKSKEAAEIRIAKAAITICFLFFASWTPYG
+VMSLIGAFGDKTLLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAISEK
+APESRAAISTSTTQEQQQTTAA
+>    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+MEPLCNASEPPLRPEARSSGNGDLQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGVF
+YIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFNSFHRGFAIY
+LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYCT
+PWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFFFSFVCPTLMILYYYSQI
+VGHVFSHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVMS
+LIGAFGDKSLLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGVNEKSGE
+ISSAQSTTTQEQQQTTAA
+>    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+MDALCNASEPPLRPEARMSSGSDELQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGV
+FYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFIYNSFHRGF
+ALGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYC
+TPWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFLFSFVVPTLMILYYYSQ
+IVGHVFNHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVM
+SLIGAFGDKSLLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGVNEKSG
+EASSAQSTTTQEQTQQTSAA
+>    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+MTNATGPQMAYYGAASMDFGYPEGVSIVDFVRPEIKPYVHQHWYNYPPVNPMWHYLLGVI
+YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCFSGGV
+WMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFALISWV
+IAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIVFSYV
+FIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQRAEIRIAKTALVNVSLWFICWTPYALI
+SLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCVHETET
+KSNDDSQSNSTVAQDKA
+>    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+MANVTGPQMAFYGSGAATFGYPEGMTVADFVPDRVKHMVLDHWYNYPPVNPMWHYLLGVV
+YLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTNFPPFCYNCFSGGR
+WMFSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNGPKLTQGKATFMCGLAWV
+ISVGWSLPPFFGWGSYTLEGILDSCSYDYFTRDMNTITYNICIFIFDFFLPASVIVFSYV
+FIVKAIFAHEAAMRAQAKKMNVTNLRSNEAETQRAEIRIAKTALVNVSLWFICWTPYAAI
+TIQGLLGNAEGITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCVHEKDP
+NDVEENQSSNTQTQEKS
+>    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
+MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKMYVPEGNLTSC
+GIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSL
+RSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLFKFEGLTPLNTIWGACFAKS
+AACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDAQSQATASEAESKA
+>    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
+MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSSIW
+CLAPAFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAA
+VSAHEKAMREQAKKMNVKSLRSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGL
+FKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDA
+QSQATASEAESKA
+>    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+MDSFAAVATQLGPQFAAPSNGSVVDKVTPDMAHLISPYWDQFPAMDPIWAKILTAYMIII
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSTIW
+CCLAPVFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIA
+AVSAHEKAMREQAKKMNVKSLRSSEDADKSAEGKLAKVALVTISLWFMAWTPYLVINCMG
+LFKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSE
+AQSQATTSEAESKA
+>    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+MERSHLPETPFDLAHSGPRFQAQSSGNGSVLDNVLPDMAHLVNPYWSRFAPMDPMMSKIL
+GLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
+ETWVLGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKILFI
+WMMAVFWTVMPLIGWSAYVPEGNLTACSIDYMTRMWNPRSYLITYSLFVYYTPLFLICYS
+YWFIIAAVAAHEKAMREQAKKMNVKSLRSSEDCDKSAEGKLAKVALTTISLWFMAWTPYL
+VICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVFGNTD
+EPKPDAPASDTETTSEADSKA
+>    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+MERSLLPEPPLAMALLGPRFEAQTGGNRSVLDNVLPDMAPLVNPHWSRFAPMDPTMSKIL
+GLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
+ETWVLGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKIAFI
+WMMAVFWTIMPLIGWSSYVPEGNLTACSIDYMTRQWNPRSYLITYSLFVYYTPLFMICYS
+YWFIIATVAAHEKAMRDQAKKMNVKSLRSSEDCDKSAENKLAKVALTTISLWFMAWTPYL
+IICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVCGTTD
+EPKPDAPPSDTETTSEAESKD
+>    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
+MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQYPPLNPMWHGILGFVIG
+MLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCMSPPMVINCYYETWVL
+GPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPLSINGALIRIIAIWLFSL
+GWTIAPMFGWNRYVPEGNMTACGTDYFNRGLLSASYLVCYGIWVYFVPLFLIIYSYWFII
+QAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVALMTISLWFMAWTPYLVINFS
+GIFNLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLACAAEPSSDAV
+STTSGTTTVTDNEKSNA
+>    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+MANQLSYSSLGWPYQPNASVVDTMPKEMLYMIHEHWYAFPPMNPLWYSILGVAMIILGII
+CVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFMMPTMTSNCFAETWILGPFMC
+EVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAAAPLTHKKATLLLLFVWIWSGGWTIL
+PFFGWSRYVPEGNLTSCTVDYLTKDWSSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAE
+HEKQLREQAKKMNVASLRANADQQKQSAECRLAKVAMMTVGLWFMAWTPYLIISWAGVFS
+SGTRLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLACGSGESGSDVKSE
+ASATTTMEEKPKIPEA
+>    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+MVESTTLVNQTWWYNPTVDIHPHWAKFDPIPDAVYYSVGIFIGVVGIIGILGNGVVIYLF
+SKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMKKWIFGKVACQLYGLLGGIFG
+FMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVWSVGPVFNWGAYVP
+EGILTSCSFDYLSTDPSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAK
+RLNAKELRKAQAGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQFGPAEWVTPYAAEL
+PVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECEDANDAEEEVVASER
+GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGYPPQGYPPQGAYPPPQGYPPQGYPP
+QGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+>    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+MGRDLRDNETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFT
+KTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGF
+MSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLWAIGPIFGWGAYTLE
+GVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKR
+LNAKELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLP
+VMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIPAGESS
+DAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGY
+PPPPQGAPPQGAPPAAPPQGVDNQAYQA
+>    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLSEVTASPAPTW
+DAPPDNASGCGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLI
+VSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAMDVMCCTASIMTLCVISIDR
+YLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGWAQNVNDDKVCLISQDFGYT
+IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDSVIALNGIVKLQKEVE
+ECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC
+IPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALK
+LAERPERPEFVLQNADYCRKKGHDS
+>    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQC
+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+>    31=p A47425 serotonin receptor 5HT-7 - rat
+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQC
+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+>    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAA
+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT
+RHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGN
+SKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
+FFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
+RQ
+>    33=p A35181 serotonin receptor class 1A - rat
+MDVFSFGQGNNTTASQEPFGTGGNVTSISDVTFSYQVITSLLLGTLIFCAVLGNACVVAA
+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT
+SLGTSSAPPPKKSLNGQPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGN
+SKEHLPLPSESGSNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
+FFIVALVLPFCESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
+RR
+>    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
+NPIIYTIFSPEFRSAFQKILFGKYRRGHR
+>    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
+NPIIYTIFSPEFRSAFQKILFGKYRRGHR
+>    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVVPNTTWWQASAPFDTPAALVR
+AAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLVMPLGAV
+YEVVQRWTLGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTNIDYIHASTAKRVGMM
+IACVWTVSFFVCIAQLLGWKDPDWNQRVSEDLRCVVSQDVGYQIFATASSFYVPVLIILI
+LYWRIYQTARKRIRRRRGATARGGVGPPPVPAGGALVAGGGSGGIAAAVVAVIGRPLPTI
+SETTTTGFTNVSSNNTSPEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKR
+ERKAAKTLAIITGAFVACWLPFFVLAILVPTCDCEVSPVLTSLSLWLGYFNSTLNPVIYT
+VFSPEFRHAFQRLLCGRRVRRRRAPQ
diff -r 8817d3a35fac -r 95526e9e3808 test-data/sample.fftns2
--- a/test-data/sample.fftns2	Tue Jun 16 10:54:16 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,504 +0,0 @@
->     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
--------------------MNGTE------------------------GDNF--------
-YVP----F-SNKTGLARSPY----------------EYPQY-------YLAEPWK-----
-----YSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-F
-TVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FR
-FGNTHAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNN
-ESYVVYMFVVHFLVPFVIIFFCYGRLLCTV----KE------------------------
----------------------------------------------------AAAAQQ---
-------------------------------------------------------------
---------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-
-HQGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC---------GKN
-PLGD-DE--SGASTSKTEVSSVS-TSPV--------------------------------
---------------------------------------------SPA-------------
-------
->     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
--------------------MNGTE------------------------GPNF--------
-YVP----F-SNITGVVRSPF----------------EQPQY-------YLAEPWQ-----
-----FSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-F
-TTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FR
-FGENHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNN
-ESFVIYMFVVHFTIPMIVIFFCYGQLVFTV----KE------------------------
----------------------------------------------------AAAQQQ---
-------------------------------------------------------------
---------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-
-HQGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC---------GKN
-PLGD-DE--ASATASKTE------TSQV--------------------------------
---------------------------------------------APA-------------
-------
->     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
--------------------MNGTE------------------------GINF--------
-YVP----M-SNKTGVVRSPF----------------EYPQY-------YLAEPWK-----
-----YRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-F
-TVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FR
-FSATHAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHN
-ESYVLYMFVIHFIIPVVVIFFSYGRLICKV----RE------------------------
----------------------------------------------------AAAQQQ---
-------------------------------------------------------------
---------------ESATTQK------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT-
-NKGA--DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICC---------GKN
-PFGD-EDVSSTVSQSKTEVSSVS-SSQV--------------------------------
---------------------------------------------SPA-------------
-------
->     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
--------------------MNGTE------------------------GKNF--------
-YVP----M-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----
-----FKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-F
-TVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FK
-FSSSHAFAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNN
-ESYVIYMFVCHFILPVAVIFFTYGRLVCTV----KA------------------------
----------------------------------------------------AAAQQQ---
-------------------------------------------------------------
---------------DSASTQK------AEREVTKMVILMVFGFLIAWTPYATVAAWIFF-
-NKGA--DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFC---------GKN
-PLGD-DE-SSTVSTSKTEVSS------V--------------------------------
---------------------------------------------SPA-------------
-------
->     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
--------------------MNGTE------------------------GNNF--------
-YVP----L-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----
-----FKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-F
-TVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FK
-FSSTHASAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNN
-ESYVLYMFICHFILPVTIIFFTYGRLVCTV----KA------------------------
----------------------------------------------------AAAQQQ---
-------------------------------------------------------------
---------------DSASTQK------AEREVTKMVILMVLGFLVAWTPYATVAAWIFF-
-NKGA--AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFC---------GKN
-PLGD-EE-SSTVSTSKTEVSS------V--------------------------------
---------------------------------------------SPA-------------
-------
->     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
--------------------MKQVPEF----------------------HEDF--------
-YIPIPLDI-NNLS--AYSPF----------------LVPQD-------HLGNQGI-----
-----FMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-S
-PLSFYSFFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-FT
-FKTPHAIAGCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSCGPDWYTTNNKYNN
-ESYVMFLFCFCFAVPFGTIVFCYGQLLITL----KL------------------------
----------------------------------------------------AAKAQA---
-------------------------------------------------------------
---------------DSASTQK------AEREVTKMVVVMVLGFLVCWAPYASFSLWIVS-
-HRGE--EFDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMM-KMVC---------GKN
--IEE-DE--ASTSSQVTQVSS------V--------------------------------
---------------------------------------------APEK------------
-------
->     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
--------------------MRKMS------------------------EEEF--------
-YL-----F-KNIS--SVGPW----------------DGPQY-------HIAPVWA-----
-----FYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-V
-FPVFVASCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-FR
-FSSKHALTVVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSCGPDWYTVGTKYRS
-ESYTWFLFIFCFIVPLSLICFSYTQLLRAL----KA------------------------
----------------------------------------------------VAAQQQ---
-------------------------------------------------------------
---------------ESATTQK------AEREVSRMVVVMVGSFCVCYVPYAAFAMYMVN-
-NRNH--GLDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIM-KMVC---------GKA
--MTD-ES--DTCSSQKTEVSTVS-STQV--------------------------------
---------------------------------------------GPN-------------
-------
->     8=opsin, greensensitive  human (fragment) S07060
-------------------------------------------------------------
-------------------------------------------------------------
---------------------------------------------------DLAETVIA-S
-TISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VR
-FDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
-QSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RA------------------------
----------------------------------------------------VAKQQK---
-------------------------------------------------------------
---------------ESESTQK------AEKEVTRMVVVMVLAFC----------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------
->     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
--------------------MAQQWSL----------QRLAGRHPQDSYEDST--------
-QSSI-FTY-TNSNS-TRGPF----------------EGPNY-------HIAPRWV-----
-----YHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-S
-TISVVNQVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-VR
-FDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
-QSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RA------------------------
----------------------------------------------------VAKQQK---
-------------------------------------------------------------
---------------ESESTQK------AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAA-
-NPGY--PFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCIL-QLF----------GKK
--VDD-GS--ELSSASKTEVSSV---SSV--------------------------------
---------------------------------------------SPA-------------
-------
->    10== Z68193   1 human Red Opsin <>[]
--------------------MAQQWSL----------QRLAGRHPQDSYEDST--------
-QSSI-FTY-TNSNS-TRGPF----------------EGPNY-------HIAPRWV-----
-----YHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-S
-TISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VR
-FDAKLAIVGIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
-QSYMIVLMVTCCIIPLAIIMLCYLQVWLAI----RA------------------------
----------------------------------------------------VAKQQK---
-------------------------------------------------------------
---------------ESESTQK------AEKEVTRMVVVMIFAYCVCWGPYTFFACFAAA-
-NPGY--AFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCIL-QLF----------GKK
--VDD-GS--ELSSASKTEVSSV---SSV--------------------------------
---------------------------------------------SPA-------------
-------
->    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
--------------------MTEAWNV----------AVFAARRSRDD-DDTT--------
-RGSV-FTY-TNTNN-TRGPF----------------EGPNY-------HIAPRWV-----
-----YNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-S
-TISVFNQIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-IK
-FDSKLAIIGIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSVELGC
-QSFMLTLMITCCFLPLFIIIVCYLQVWMAI----RA------------------------
----------------------------------------------------VAAQQK---
-------------------------------------------------------------
---------------ESESTQK------AEREVSRMVVVMIVAFCICWGPYASFVSFAAA-
-NPGY--AFHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIM-QLF----------GKK
--VDD-GS--EASTTSRTEVSSVS-NSSV--------------------------------
---------------------------------------------APA-------------
-------
->    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
--------------------MA-AWEA----------AFAARRRHEE--EDTT--------
-RDSV-FTY-TNSNN-TRGPF----------------EGPNY-------HIAPRWV-----
-----YNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-S
-TISVINQIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-IK
-FDGKLAVAGILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSDPGV
-QSYMVVLMVTCCFFPLAIIILCYLQVWLAI----RA------------------------
----------------------------------------------------VAAQQK---
-------------------------------------------------------------
---------------ESESTQK------AEKEVSRMVVVMIVAYCFCWGPYTFFACFAAA-
-NPGY--AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIL-QLF----------GKK
--VDD-GS--EVST-SRTEVSSVS-NSSV--------------------------------
---------------------------------------------SPA-------------
-------
->    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
--------------------MS---------------------------SNSS--------
-QAP--------PNG-TPGPF----------------DGPQW------PYQAPQST-----
-----YVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-S
-SVSLSNNIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-FQ
-FQRRHAVSGCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSCGPNWYTGGSNN--
-NSYILSLFVTCFVLPLSLILFSYTNLLLTL----RA------------------------
----------------------------------------------------AAAQQK---
-------------------------------------------------------------
---------------EADTTQR------AEREVTRMVIVMVMAFLLCWLPYSTFALVVAT-
-HKGI--IIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLL-EMLCCGY-----QPQR
--TGK-AS--PGTPGPHADVTAAGLRNKV--------------------------------
---------------------------------------------MPAHP---V-------
-------
->    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
-----------MESGNVSSSLFGNVST----------ALRPEARL----SA----------
--ETRLLGW--------NVPP----------------EELR--------HIPEHWLTYPEP
-PESMNYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--T
-PIFIYNSFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--K
-MTHGKAIAMIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSCTFDYLT--DNFDT
-RLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA------------------------
----------------------------------------------------LRDQAKKM-
---------------------------------NVESL-----------------------
------------RSNVDKNKET------AEIRIAKAAITICFLFFCSWTPYGVMSLIGAF-
-GDKT--LLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLAL--------N
-EKAP-ES-SAVASTSTTQEP-QQ-TTAA--------------------------------
-------------------------------------------------------------
-------
->    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
-----------MEYHNVSSVL-GNVSS----------VLRPDARL----SA----------
--ESRLLGW--------NVPP----------------DELR--------HIPEHWLIYPEP
-PESMNYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--T
-PIFIYNSFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--K
-MTHGKAIAMIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSCTFDYLT--DNFDT
-RLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA------------------------
----------------------------------------------------LRDQAKKM-
---------------------------------NVDSL-----------------------
------------RSNVDKSKEA------AEIRIAKAAITICFLFFASWTPYGVMSLIGAF-
-GDKT--LLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAI--------S
-EKAP-ES-RAAISTSTTQEQ-QQ-TTAA--------------------------------
-------------------------------------------------------------
-------
->    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
-----------ME------PLCNASEP----------PLRPEAR-----SSGN--------
-GDLQFLGW--------NVPP----------------DQIQ--------YIPEHWLTQLEP
-PASMHYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--A
-PIF--NSFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--N
-MTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDT
-RLFVGTIFFFSFVCPTLMILYYYSQIVGHVFSHEKA------------------------
----------------------------------------------------LREQAKKM-
---------------------------------NVESL-----------------------
------------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-
-GDKS--LLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGV--------N
-EKSG-EI-SSAQST-TTQEQ-QQ-TTAA--------------------------------
-------------------------------------------------------------
-------
->    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
-----------MD------ALCNASEP----------PLRPEARM----SSGS--------
-DELQFLGW--------NVPP----------------DQIQ--------YIPEHWLTQLEP
-PASMHYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--A
-PIFIYNSFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--N
-MTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDT
-RLFVGTIFLFSFVVPTLMILYYYSQIVGHVFNHEKA------------------------
----------------------------------------------------LREQAKKM-
---------------------------------NVESL-----------------------
------------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-
-GDKS--LLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGV--------N
-EKSG-EA-SSAQST-TTQEQTQQ-TSAA--------------------------------
-------------------------------------------------------------
-------
->    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
--------------------MTNATGP----------QMAYYGAA----SMD---------
------FGYPEGVSIVDFVRP----------------EIKP--------YVHQHWYNYPPV
-NPMWHYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-V
-PFFTYNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-PK
-LTTGKAVVFALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSCSYDYLT--QDFNT
-FSYNIFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAA------------------------
----------------------------------------------------MRAQAKKM-
---------------------------------NVSTL-----------------------
------------RS-NEADAQR------AEIRIAKTALVNVSLWFICWTPYALISLKGVM-
-GDTS--GITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCV------HET
-ETKS-ND-DSQSNSTVAQDKA---------------------------------------
-------------------------------------------------------------
-------
->    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
--------------------MANVTGP----------QMAFYGSG----AAT---------
------FGYPEGMTVADFVPD----------------RVKH--------MVLDHWYNYPPV
-NPMWHYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-F
-PPFCYNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-PK
-LTQGKATFMCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSCSYDYFT--RDMNT
-ITYNICIFIFDFFLPASVIVFSYVFIVKAIFAHEAA------------------------
----------------------------------------------------MRAQAKKM-
---------------------------------NVTNL-----------------------
------------RS-NEAETQR------AEIRIAKTALVNVSLWFICWTPYAAITIQGLL-
-GNAE--GITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCV------HEK
-DPND-VE-ENQSSNTQTQEKS---------------------------------------
-------------------------------------------------------------
-------
->    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
-----------ME---SFAVAAAQLGP----------HFAPLS------------------
-----------NGSVVDKVTP----------------DMAH--------LISPYWNQFPAM
-DPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
-PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
-MTIPLALGKM---------------------------YVPEGNLTSCGIDYLE--RDWNP
-RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
----------------------------------------------------MREQAKKM-
---------------------------------NVKSL-----------------------
------------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-
-KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
-DDGK-SS-DAQSQATASEAESKA-------------------------------------
-------------------------------------------------------------
-------
->    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
-----------ME---SFAVAAAQLGP----------HFAPLS------------------
-----------NGSVVDKVTP----------------DMAH--------LISPYWNQFPAM
-DPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
-PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
-MTIPLALGKIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSCGIDYLE--RDWNP
-RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
----------------------------------------------------MREQAKKM-
---------------------------------NVKSL-----------------------
------------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-
-KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
-DDGK-SS-DAQSQATASEAESKA-------------------------------------
-------------------------------------------------------------
-------
->    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
-----------MD---SFAAVATQLGP----------QFAAPS------------------
-----------NGSVVDKVTP----------------DMAH--------LISPYWDQFPAM
-DPIWAKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
-PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
-MTIPLALGKIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSCGIDYLE--RDWNP
-RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
----------------------------------------------------MREQAKKM-
---------------------------------NVKSL-----------------------
------------RS-SEDADKS------AEGKLAKVALVTISLWFMAWTPYLVINCMGLF-
-KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
-DDGK-SS-EAQSQATTSEAESKA-------------------------------------
-------------------------------------------------------------
-------
->    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
------MERSHLP---ETPFDLAHSGP----------RFQAQSSG----------------
-----------NGSVLDNVLP----------------DMAH--------LVNPYWSRFAPM
-DPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-S
-PVMIINFYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-TP
-MTIKTSIMKILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTACSIDYMT--RMWNP
-RSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKA------------------------
----------------------------------------------------MREQAKKM-
---------------------------------NVKSL-----------------------
------------RS-SEDCDKS------AEGKLAKVALTTISLWFMAWTPYLVICYFGLF-
-KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVF------GNT
-DEPKPDA-PASDTETTSEADSKA-------------------------------------
-------------------------------------------------------------
-------
->    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
------MERSLLP---EPPLAMALLGP----------RFEAQTGG----------------
-----------NRSVLDNVLP----------------DMAP--------LVNPHWSRFAPM
-DPTMSKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-S
-PVMIINFYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-TP
-MTIKTSIMKIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTACSIDYMT--RQWNP
-RSYLITYSLFVYYTPLFMICYSYWFIIATVAAHEKA------------------------
----------------------------------------------------MRDQAKKM-
---------------------------------NVKSL-----------------------
------------RS-SEDCDKS------AENKLAKVALTTISLWFMAWTPYLIICYFGLF-
-KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVC------GTT
-DEPKPDA-PPSDTETTSEAESKD-------------------------------------
-------------------------------------------------------------
-------
->    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
--------------------MIAVSGP----------SYEAFSYG----GQA---------
-----RF---NNQTVVDKVPP----------------DMLH--------LIDANWYQYPPL
-NPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-S
-PPMVINCYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-KP
-LSINGALIRIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTACGTDYFN--RGLLS
-ASYLVCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKN------------------------
----------------------------------------------------MREQAKKM-
---------------------------------NVASL-----------------------
------------RS-SENQNTS------AECKLAKVALMTISLWFMAWTPYLVINFSGIF-
-NL-V--KISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLAC-------AA
-EPSS-DA-VSTTSGTTTVTDNEK-SNA---------------------------------
-------------------------------------------------------------
-------
->    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
----------------------MANQL----------SYSSLGWP----YQP---------
-----------NASVVDTMPK----------------EMLY--------MIHEHWYAFPPM
-NPLWYSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-M
-PTMTSNCFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-AP
-LTHKKATLLLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSCTVDYLT--KDWSS
-ASYVVIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQ------------------------
----------------------------------------------------LREQAKKM-
---------------------------------NVASL-----------------------
------------RANADQQKQS------AECRLAKVAMMTVGLWFMAWTPYLIISWAGVF-
-SSGT--RLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLAC------GSG
-ESGS-DV-KSEASATTTMEEKPK-IPEA--------------------------------
-------------------------------------------------------------
-------
->    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
-------------------------------------MVESTTLV----NQT---------
------WWY--NPTVD----------------------------------IHPHWAKFDPI
-PDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGF
-PLKTISAFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKK
-MSHRRAFLMIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSCSFDYLS--TDPST
-RSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKE------------------------
----------------------------------------------------MAAMAKRL-
---------------------------------NAKEL-----------------------
------------R--KAQAGAS------AEMKLAKISMVIITQFMLSWSPYAIIALLAQF-
-GPAE--WVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKEC
-EDAN-DA-EEEVVASER--GGES-RDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PP
-QGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQG---VDNQAYQA
-------
->    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
--------------------------------------MGRDLRD----NET---------
------WWY--NPSIV----------------------------------VHPHWREFDQV
-PDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGF
-PLMTISCFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKK
-MSHRRAFIMIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNCSFDYIS--RDSTT
-RSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKE------------------------
----------------------------------------------------MAAMAKRL-
---------------------------------NAKEL-----------------------
------------R--KAQAGAN------AEMRLAKISIVIVSQFLLSWSPYAVVALLAQF-
-GPLE--WVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKET
-EDDK-DA-ETEIPAGESSDAAPS-ADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPP
-QGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQG---VDNQAYQA
-------
->    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
----------MMD-------VNSSGRPDLYGHLRSF-LLPEVGRGLPDLSPDGGADPVAGS
-WAPHLLS---EVTASPAPTW----------------DAPPDNASGCGEQIN--------Y
-GRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-M
-PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
-QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
--GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
-----------------------------------P--------GFPR----VEPDS----
----VIAL-----------------NGIVKLQ--------KEVEECAN-------------
------LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
-CGTSCSCIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR---------
------NINRKLSAAGMHEALKLA-------------------------------------
--------------------------------------------ERPERPEFVLQNADYCR
-KKGHDS
->    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
-------------------------------------------------------------
--MPHLLSGFLEVTASPAPTW----------------DAPPDNVSGCGEQIN--------Y
-GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-M
-PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
-QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
--GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
-----------------------------------P--------GFPR----VQPES----
----VISL-----------------NGVVKLQ--------KEVEECAN-------------
------LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
-CGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQCQYR---------
------NINRKLSAAGMHEALKLA-------------------------------------
--------------------------------------------ERPERSEFVLQNSDHCG
-KKGHDT
->    31=p A47425 serotonin receptor 5HT-7 - rat
-------------------------------------------------------------
--MPHLLSGFLEVTASPAPTW----------------DAPPDNVSGCGEQIN--------Y
-GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-M
-PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
-QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
--GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
-----------------------------------P--------GFPR----VQPES----
----VISL-----------------NGVVKLQ--------KEVEECAN-------------
------LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
-CGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR---------
------NINRKLSAAGMHEALKLA-------------------------------------
--------------------------------------------ERPERSEFVLQNSDHCG
-KKGHDT
->    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
-----------MD-------VLSPG------------QGNNTTSPPAPFETGG--------
-----------NTTGISDVTV----------------------------------------
---SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L
-PMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK
-RTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH---------
--GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------
----------------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR-
---------NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAG-
--PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-
-CESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------
------RQ-----------------------------------------------------
-------------------------------------------------------------
-------
->    33=p A35181 serotonin receptor class 1A - rat
-----------MD-------VFSFG------------QGNNTTASQEPFGTGG--------
-----------NVTSISDVTF----------------------------------------
---SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L
-PMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK
-RTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH---------
--GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------
----------------TVRKVEKKGAGTSLGTSSAPPPKKS-----------LNGQPGSG-
---------DWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESG-
--SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-
-CESSC-HMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------
------RR-----------------------------------------------------
-------------------------------------------------------------
-------
->    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
-MANFTFGDLALD-------VARMG-----GLASTPSGLRSTGLTTPGLSPTG--------
-----------LVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVY
-SHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-M
-PLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRR
-RSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK---------
--GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTE
-YSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS--
---------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS-
-------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-
-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------
------RGHR---------------------------------------------------
-------------------------------------------------------------
-------
->    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
-MANFTFGDLALD-------VARMG-----GLASTPSGLRSTGLTTPGLSPTG--------
-----------LVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVY
-SHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-M
-PLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRR
-RSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK---------
--GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTE
-YSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS--
---------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS-
-------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-
-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------
------RGHR---------------------------------------------------
-------------------------------------------------------------
-------
->    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
--MEGAEGQEELD-------WEAL-------YLRLP--LQNCSWNSTGWEPNW--------
-----------NVTVVPNTTW---------WQASAPFDTPAALVRAAAK------------
---------AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-M
-PLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHA
-STAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV---------
--GYQIFATASSFYVPVLIILILYWRIYQTARKRIR-------------------------
---------------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGI
-AAAVVAVIGRPLPTISETTTTGFTNVSS----NNTS---PEKQSCANGLEADPPTTGYGA
-VAAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-
-CDCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRV---------
------RRRRA--------------------------------------------------
----------------------------------------------PQ-------------
-------
diff -r 8817d3a35fac -r 95526e9e3808 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 16 10:54:16 2015 -0400
+++ b/tool_dependencies.xml	Fri Jul 31 19:00:37 2015 -0400
@@ -11,6 +11,7 @@
                 <action type="shell_command">sed -i "s|\(PREFIX = \).*$|\1$INSTALL_DIR|" Makefile</action>
                 <action type="shell_command">make clean; make; make install</action>
                 <action type="set_environment">
+                    <environment_variable name="MAFFT_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>