JAL-1819 Test cases for Identify file

[jalview.git] / examples / test.pileup

diff --git a/examples/test.pileup b/examples/test.pileup
new file mode 100644 (file)
index 0000000..d191e4b
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+++ b/examples/test.pileup
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+PileUp
+
+   MSF: 157   Type: P    Check:  1935   ..
+
+
+ Name: FER_CAPAA/1-97 oo  Len:  157  Check:  5701  Weight:  1.00
+ Name: FER_CAPAN/1-144 oo  Len:  157  Check:  8823  Weight:  1.00
+ Name: FER1_SOLLC/1-144 oo  Len:  157  Check:  41  Weight:  1.00
+ Name: Q93XJ9_SOLTU/1-144 oo  Len:  157  Check:  466  Weight:  1.00
+ Name: FER1_PEA/1-149 oo  Len:  157  Check:  5889  Weight:  1.00
+ Name: Q7XA98_TRIPR/1-152 oo  Len:  157  Check:  1438  Weight:  1.00
+ Name: FER1_MESCR/1-148 oo  Len:  157  Check:  3943  Weight:  1.00
+ Name: FER1_SPIOL/1-147 oo  Len:  157  Check:  2139  Weight:  1.00
+ Name: FER3_RAPSA/1-96 oo  Len:  157  Check:  7694  Weight:  1.00
+ Name: FER1_ARATH/1-148 oo  Len:  157  Check:  6163  Weight:  1.00
+ Name: FER_BRANA/1-96 oo  Len:  157  Check:  6628  Weight:  1.00
+ Name: FER2_ARATH/1-148 oo  Len:  157  Check:  7866  Weight:  1.00
+ Name: Q93Z60_ARATH/1-118 oo  Len:  157  Check:  3003  Weight:  1.00
+ Name: FER1_MAIZE/1-150 oo  Len:  157  Check:  4097  Weight:  1.00
+ Name: O80429_MAIZE/1-140 oo  Len:  157  Check:  1696  Weight:  1.00
+ Name: 1A70|/1-97 oo  Len:  156  Check:  6348  Weight:  1.00
+
+
+//
+
+FER_CAPAA/1-97 ---------- ---------- ---------- ---------- ----------
+FER_CAPAN/1-144 MA------SV SATMISTSFM PRKPAVTSL- KPIPNVGE-- ALFGLKS-A-
+FER1_SOLLC/1-144 MA------SI SGTMISTSFL PRKPAVTSL- KAISNVGE-- ALFGLKS-G-
+Q93XJ9_SOLTU/1-144 MA------SI SGTMISTSFL PRKPVVTSL- KAISNVGE-- ALFGLKS-G-
+FER1_PEA/1-149 MATT---PAL YGTAVSTSFL RTQPMPMSV- TTTKAFSN-- GFLGLKT-SL
+Q7XA98_TRIPR/1-152 MATT---PAL YGTAVSTSFM RRQPVPMSV- ATTTTTKAFP SGFGLKSVST
+FER1_MESCR/1-148 MAAT--TAAL SGATMSTAFA PK--TPPMTA ALPTNVGR-- ALFGLKS-SA
+FER1_SPIOL/1-147 MAAT--TTTM MG--MATTFV PKPQAPPMMA ALPSNTGR-- SLFGLKT-GS
+FER3_RAPSA/1-96 ---------- ---------- ---------- ---------- ----------
+FER1_ARATH/1-148 MAST----AL SSAIVGTSFI RRSPAPISLR SLPSANTQ-- SLFGLKS-GT
+FER_BRANA/1-96 ---------- ---------- ---------- ---------- ----------
+FER2_ARATH/1-148 MAST----AL SSAIVSTSFL RRQQTPISLR SLPFANTQ-- SLFGLKS-ST
+Q93Z60_ARATH/1-118 MAST----AL SSAIVSTSFL RRQQTPISLR SLPFANTQ-- SLFGLKS-ST
+FER1_MAIZE/1-150 MATVLGSPRA PAFFFSSSSL RAAPAPTAV- -ALPAAKV-- GIMGRSA-SS
+O80429_MAIZE/1-140 MAAT------ ---ALSMSIL R---APPPCF SSPLRLRV-- AVAKPLA-AP
+1A70|/1-97   ---------- ---------- ---------- ---------- ----------
+
+FER_CAPAA/1-97 ---------A SYKVKLITPD GPIEFDCPDD VYILDQAEEA GHDLPYSCRA
+FER_CAPAN/1-144 -NGGKVTCMA SYKVKLITPD GPIEFDCPDN VYILDQAEEA GHDLPYSCRA
+FER1_SOLLC/1-144 -RNGRITCMA SYKVKLITPE GPIEFECPDD VYILDQAEEE GHDLPYSCRA
+Q93XJ9_SOLTU/1-144 -RNGRITCMA SYKVKLITPD GPIEFECPDD VYILDQAEEE GHDLPYSCRA
+FER1_PEA/1-149 KRGDLAVAMA SYKVKLVTPD GTQEFECPSD VYILDHAEEV GIDLPYSCRA
+Q7XA98_TRIPR/1-152 KRGDLAVAMA TYKVKLITPE GPQEFDCPDD VYILDHAEEV GIELPYSCRA
+FER1_MESCR/1-148 SR-GRVTAMA AYKVTLVTPE GKQELECPDD VYILDAAEEA GIDLPYSCRA
+FER1_SPIOL/1-147 R--GGRMTMA AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA
+FER3_RAPSA/1-96 ---------A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA
+FER1_ARATH/1-148 ARGGRVTAMA TYKVKFITPE GELEVECDDD VYVLDAAEEA GIDLPYSCRA
+FER_BRANA/1-96 ---------A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA
+FER2_ARATH/1-148 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA
+Q93Z60_ARATH/1-118 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA
+FER1_MAIZE/1-150 RR--RLRAQA TYNVKLITPE GEVELQVPDD VYILDQAEED GIDLPYSCRA
+O80429_MAIZE/1-140 MRRQLLRAQA TYNVKLITPE GEVELQVPDD VYILDFAEEE GIDLPFSCRA
+1A70|/1-97   ---------A AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA
+
+FER_CAPAA/1-97 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK
+FER_CAPAN/1-144 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK
+FER1_SOLLC/1-144 GSCSSCAGKV TAGSVDQSDG NFLDEDQEAA GFVLTCVAYP KGDVTIETHK
+Q93XJ9_SOLTU/1-144 GSCSSCAGKV TAGTVDQSDG KFLDDDQEAA GFVLTCVAYP KCDVTIETHK
+FER1_PEA/1-149 GSCSSCAGKV VGGEVDQSDG SFLDDEQIEA GFVLTCVAYP TSDVVIETHK
+Q7XA98_TRIPR/1-152 GSCSSCAGKV VNGNVNQEDG SFLDDEQIEG GWVLTCVAFP TSDVTIETHK
+FER1_MESCR/1-148 GSCSSCAGKV TSGSVNQDDG SFLDDDQIKE GWVLTCVAYP TGDVTIETHK
+FER1_SPIOL/1-147 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK
+FER3_RAPSA/1-96 GSCSSCAGKV VSGSVDQSDQ SFLDDDQIAE GFVLTCAAYP TSDVTIETHR
+FER1_ARATH/1-148 GSCSSCAGKV VSGSVDQSDQ SFLDDEQIGE GFVLTCAAYP TSDVTIETHK
+FER_BRANA/1-96 GSCSSCAGKV VSGFVDQSDE SFLDDDQIAE GFVLTCAAYP TSDVTIETHK
+FER2_ARATH/1-148 GSCSSCAGKV VSGSIDQSDQ SFLDDEQMSE GYVLTCVAYP TSDVVIETHK
+Q93Z60_ARATH/1-118 GSCSSCAGKV VSGSIDQSDQ SFLDD----- ---------- ----------
+FER1_MAIZE/1-150 GSCSSCAGKV VSGSVDQSDQ SYLDDGQIAD GWVLTCHAYP TSDVVIETHK
+O80429_MAIZE/1-140 GSCSSCAGKV VSGSVDQSDQ SFLNDNQVAD GWVLTCAAYP TSDVVIETHK
+1A70|/1-97   GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK
+
+FER_CAPAA/1-97 EAELVG-
+FER_CAPAN/1-144 EAELVG-
+FER1_SOLLC/1-144 EEELTA-
+Q93XJ9_SOLTU/1-144 EEELTA-
+FER1_PEA/1-149 EEDLTA-
+Q7XA98_TRIPR/1-152 EEELTA-
+FER1_MESCR/1-148 EEELTA-
+FER1_SPIOL/1-147 EEELTA-
+FER3_RAPSA/1-96 EEDMV--
+FER1_ARATH/1-148 EEDIV--
+FER_BRANA/1-96 EEELV--
+FER2_ARATH/1-148 EEAIM--
+Q93Z60_ARATH/1-118 -------
+FER1_MAIZE/1-150 EEELTGA
+O80429_MAIZE/1-140 EDDLL--
+1A70|/1-97   KEELTA
+