JAL-1819 Test cases for Identify file

[jalview.git] / examples / test.msf

diff --git a/examples/test.msf b/examples/test.msf
new file mode 100644 (file)
index 0000000..8a476aa
--- /dev/null
+++ b/examples/test.msf
@@ -0,0 +1,93 @@
+!!AA_MULTIPLE_ALIGNMENT 1.0
+
+   MSF: 157   Type: P    Check:  4683   ..
+
+
+  Name: FER_CAPAA/1-157    Len: 157  Check: 3320  Weight: 1.00
+  Name: FER_CAPAN/1-145    Len: 157  Check: 2597  Weight: 1.00
+  Name: FER1_SOLLC/1-145   Len: 157  Check: 3815  Weight: 1.00
+  Name: Q93XJ9_SOLTU/1-145 Len: 157  Check: 4240  Weight: 1.00
+  Name: FER1_PEA/1-150     Len: 157  Check: 9547  Weight: 1.00
+  Name: Q7XA98_TRIPR/1-153 Len: 157  Check: 4969  Weight: 1.00
+  Name: FER1_MESCR/1-149   Len: 157  Check: 7664  Weight: 1.00
+  Name: FER1_SPIOL/1-148   Len: 157  Check: 5892  Weight: 1.00
+  Name: FER3_RAPSA/1-157   Len: 157  Check: 8715  Weight: 1.00
+  Name: FER1_ARATH/1-150   Len: 157  Check: 3201  Weight: 1.00
+  Name: FER_BRANA/1-157    Len: 157  Check: 7649  Weight: 1.00
+  Name: FER2_ARATH/1-150   Len: 157  Check: 4904  Weight: 1.00
+  Name: Q93Z60_ARATH/1-150 Len: 157  Check: 4436  Weight: 1.00
+  Name: FER1_MAIZE/1-150   Len: 157  Check: 4392  Weight: 1.00
+  Name: O80429_MAIZE/1-142 Len: 157  Check: 8858  Weight: 1.00
+  Name: 1A70|/1-156        Len: 156  Check:  484  Weight: 1.00
+
+
+//
+
+FER_CAPAA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
+FER_CAPAN/1-145 MA......SV SATMISTSFM PRKPAVTSL. KPIPNVGE.. ALFGLKS.A.
+FER1_SOLLC/1-145 MA......SI SGTMISTSFL PRKPAVTSL. KAISNVGE.. ALFGLKS.G.
+Q93XJ9_SOLTU/1-145 MA......SI SGTMISTSFL PRKPVVTSL. KAISNVGE.. ALFGLKS.G.
+FER1_PEA/1-150 MATT...PAL YGTAVSTSFL RTQPMPMSV. TTTKAFSN.. GFLGLKT.SL
+Q7XA98_TRIPR/1-153 MATT...PAL YGTAVSTSFM RRQPVPMSV. ATTTTTKAFP SGFGLKSVST
+FER1_MESCR/1-149 MAAT..TAAL SGATMSTAFA PK..TPPMTA ALPTNVGR.. ALFGLKS.SA
+FER1_SPIOL/1-148 MAAT..TTTM MG..MATTFV PKPQAPPMMA ALPSNTGR.. SLFGLKT.GS
+FER3_RAPSA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
+FER1_ARATH/1-150 MAST....AL SSAIVGTSFI RRSPAPISLR SLPSANTQ.. SLFGLKS.GT
+FER_BRANA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
+FER2_ARATH/1-150 MAST....AL SSAIVSTSFL RRQQTPISLR SLPFANTQ.. SLFGLKS.ST
+Q93Z60_ARATH/1-150 MAST....AL SSAIVSTSFL RRQQTPISLR SLPFANTQ.. SLFGLKS.ST
+FER1_MAIZE/1-150 MATVLGSPRA PAFFFSSSSL RAAPAPTAV. .ALPAAKV.. GIMGRSA.SS
+O80429_MAIZE/1-142 MAAT...... ...ALSMSIL R...APPPCF SSPLRLRV.. AVAKPLA.AP
+1A70|/1-156  ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
+
+FER_CAPAA/1-157 ~~~~~~~~~A SYKVKLITPD GPIEFDCPDD VYILDQAEEA GHDLPYSCRA
+FER_CAPAN/1-145 .NGGKVTCMA SYKVKLITPD GPIEFDCPDN VYILDQAEEA GHDLPYSCRA
+FER1_SOLLC/1-145 .RNGRITCMA SYKVKLITPE GPIEFECPDD VYILDQAEEE GHDLPYSCRA
+Q93XJ9_SOLTU/1-145 .RNGRITCMA SYKVKLITPD GPIEFECPDD VYILDQAEEE GHDLPYSCRA
+FER1_PEA/1-150 KRGDLAVAMA SYKVKLVTPD GTQEFECPSD VYILDHAEEV GIDLPYSCRA
+Q7XA98_TRIPR/1-153 KRGDLAVAMA TYKVKLITPE GPQEFDCPDD VYILDHAEEV GIELPYSCRA
+FER1_MESCR/1-149 SR.GRVTAMA AYKVTLVTPE GKQELECPDD VYILDAAEEA GIDLPYSCRA
+FER1_SPIOL/1-148 R..GGRMTMA AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA
+FER3_RAPSA/1-157 ~~~~~~~~~A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA
+FER1_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GELEVECDDD VYVLDAAEEA GIDLPYSCRA
+FER_BRANA/1-157 ~~~~~~~~~A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA
+FER2_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA
+Q93Z60_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA
+FER1_MAIZE/1-150 RR..RLRAQA TYNVKLITPE GEVELQVPDD VYILDQAEED GIDLPYSCRA
+O80429_MAIZE/1-142 MRRQLLRAQA TYNVKLITPE GEVELQVPDD VYILDFAEEE GIDLPFSCRA
+1A70|/1-156  ~~~~~~~~~A AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA
+
+FER_CAPAA/1-157 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK
+FER_CAPAN/1-145 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK
+FER1_SOLLC/1-145 GSCSSCAGKV TAGSVDQSDG NFLDEDQEAA GFVLTCVAYP KGDVTIETHK
+Q93XJ9_SOLTU/1-145 GSCSSCAGKV TAGTVDQSDG KFLDDDQEAA GFVLTCVAYP KCDVTIETHK
+FER1_PEA/1-150 GSCSSCAGKV VGGEVDQSDG SFLDDEQIEA GFVLTCVAYP TSDVVIETHK
+Q7XA98_TRIPR/1-153 GSCSSCAGKV VNGNVNQEDG SFLDDEQIEG GWVLTCVAFP TSDVTIETHK
+FER1_MESCR/1-149 GSCSSCAGKV TSGSVNQDDG SFLDDDQIKE GWVLTCVAYP TGDVTIETHK
+FER1_SPIOL/1-148 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK
+FER3_RAPSA/1-157 GSCSSCAGKV VSGSVDQSDQ SFLDDDQIAE GFVLTCAAYP TSDVTIETHR
+FER1_ARATH/1-150 GSCSSCAGKV VSGSVDQSDQ SFLDDEQIGE GFVLTCAAYP TSDVTIETHK
+FER_BRANA/1-157 GSCSSCAGKV VSGFVDQSDE SFLDDDQIAE GFVLTCAAYP TSDVTIETHK
+FER2_ARATH/1-150 GSCSSCAGKV VSGSIDQSDQ SFLDDEQMSE GYVLTCVAYP TSDVVIETHK
+Q93Z60_ARATH/1-150 GSCSSCAGKV VSGSIDQSDQ SFLDD~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
+FER1_MAIZE/1-150 GSCSSCAGKV VSGSVDQSDQ SYLDDGQIAD GWVLTCHAYP TSDVVIETHK
+O80429_MAIZE/1-142 GSCSSCAGKV VSGSVDQSDQ SFLNDNQVAD GWVLTCAAYP TSDVVIETHK
+1A70|/1-156  GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK
+
+FER_CAPAA/1-157 EAELVG~
+FER_CAPAN/1-145 EAELVG~
+FER1_SOLLC/1-145 EEELTA~
+Q93XJ9_SOLTU/1-145 EEELTA~
+FER1_PEA/1-150 EEDLTA~
+Q7XA98_TRIPR/1-153 EEELTA~
+FER1_MESCR/1-149 EEELTA~
+FER1_SPIOL/1-148 EEELTA~
+FER3_RAPSA/1-157 EEDMV~~
+FER1_ARATH/1-150 EEDIV~~
+FER_BRANA/1-157 EEELV~~
+FER2_ARATH/1-150 EEAIM~~
+Q93Z60_ARATH/1-150 ~~~~~~~
+FER1_MAIZE/1-150 EEELTGA
+O80429_MAIZE/1-142 EDDLL~~
+1A70|/1-156  KEELTA
+