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JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.
[jabaws.git] / binaries / src / tcoffee / example / prf3.aln
diff --git a/binaries/src/tcoffee/example/prf3.aln b/binaries/src/tcoffee/example/prf3.aln
new file mode 100644 (file)
index 0000000..350ca0a
--- /dev/null
+++ b/binaries/src/tcoffee/example/prf3.aln
@@ -0,0 +1,148 @@
+CLUSTAL FORMAT for T-COFFEE Version_4.32 [http://www.tcoffee.org], CPU=24.75 sec, SCORE=62, Nseq=22, Len=305 
+
+sp|P00746|CFAD_HUMAN   M-HSSVY-FAVLVLLGAAACA-----ARPRGR----------ILGGREAEAHARPYMASV
+sp|P51779|CFAD_PIG     MADRSGH-LAALILLGAAVCV-----AQPRGR----------ILGGQEAKSHERPYMASV
+sp|P15119|MCPT2_MOUSE  M-------QALLFLMALLLPS-----GAGAEE----------IIGGVEAKPHSRPYMAYL
+sp|Q00356|MCPTX_MOUSE  M-------QALLFLMALLLPS-----GAGAEE----------IIGGVESEPHSRPYMAYV
+sp|P21844|MCPT5_MOUSE  M------HLLTLHLLLLLLGS-----STKAGE----------IIGGTECIPHSRPYMAYL
+sp|P50339|MCPT3_RAT    M------NLHALCLLLLLLGS-----STKAGE----------IIGGTECIPHSRPYMAYL
+sp|P50341|MCPT2_MERUN  M------HLLALHLLLFLLGS-----RAKAGE----------IIGGTECKPHSRPYMAYL
+sp|P24158|PRTN3_HUMAN  MAHRPPSPALASVLLALLLSG-----AARAAE----------IVGGHEAQPHSRPYMASL
+sp|Q9H2R5|KLK15_HUMAN  M-W-----LLLTLSFLLASTA-----AQDGDK----------LLEGDECAPHSQPWQVAL
+sp|Q9UKR3|KLK13_HUMAN  M-WPLAL-VIASLTLALSGGV-----SQESSKVLNTNGTSGFLPGGYTCFPHSQPWQAAL
+sp|P16049|TRY1_GADMO   M----KS-LIFVLLL--GAVF------AEEDK----------IVGGYECTKHSQAHQVSL
+sp|Q91041|TRYX_GADMO   M----KS-LIFVLLL--GAVF------AEEDK----------IVGGYECTRHSQAHQVSL
+sp|P35031|TRY1_SALSA   M----IS-LVFVLLI--GAAF-----ATEDDK----------IVGGYECKAYSQTHQVSL
+sp|P35032|TRY2_SALSA   ------------------AAF-----ATEDDK----------IVGGYECKAYSQPHQVSL
+sp|P35033|TRY3_SALSA   F------------AVAFAAPI-----DDEDDK----------IVGGYECRKNSASYQASL
+sp|Q90627|TRY1_CHICK   M----KF-LVLVAFV--GVTVAFPISDEDDDK----------IVGGYSCARSAAPYQVSL
+sp|P00761|TRYP_PIG     F----------------------PT-DD-DDK----------IVGGYTCAANSIPYQVSL
+sp|P08426|TRY3_RAT     M----KA-LIFLAFL--GAAVALPL-DDDDDK----------IVGGYTCQKNSLPYQVSL
+sp|P00762|TRY1_RAT     M----SA-LLILALV--GAAVAFPL-ED-DDK----------IVGGYTCPEHSVPYQVSL
+sp|P06872|TRY2_CANFA   M----NP-LLILAFL--GAAVATPT-DD-DDK----------IVGGYTCEENSVPYQVSL
+sp|P07477|TRY1_HUMAN   M----NP-LLILTFV--AAALAAPF-DD-DDK----------IVGGYNCEENSVPYQVSL
+sp|P70059|TRY2_XENLA   M----KF-LVILVLL--GAAVAF---ED-DDK----------IVGGFTCAKNAVPYQVSL
+                                                      .          :  *  .     .  . :
+
+sp|P00746|CFAD_HUMAN   QL----NGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLR
+sp|P51779|CFAD_PIG     QV----NGKHVCGGFLVSEQWVLSAAHCLEDVAEGKLQVLLGAHSLSQPEPSKRLYDVLR
+sp|P15119|MCPT2_MOUSE  KFTTKNGSKERCGGFLIAPQFVMTAAHCN----GSEISVILGAHNINKNEPTQQIIKTEK
+sp|Q00356|MCPTX_MOUSE  NTFRRKGYVAICGGFLITPQFVMTAAHCR----GRRMTVTLGAHNVRKRECTQQKIKVEK
+sp|P21844|MCPT5_MOUSE  EIVTSENYLSACSGFLIRRNFVLTAAHCA----GRSITVLLGAHNKTSKEDTWQKLEVEK
+sp|P50339|MCPT3_RAT    EIVTSDNYLSACSGFLIRRNFVLTAAHCA----GRSITVLLGAHNKTYKEDTWQKLEVEK
+sp|P50341|MCPT2_MERUN  EIATSKNYLSTCSGFLIRRNFVLTAAHCS----GRSITVLLGAHNKTAKEDTWQKIEVEK
+sp|P24158|PRTN3_HUMAN  QMRGNPGS-HFCGGTLIHPSFVLTAAHCLRDIPQRLVNVVLGAHNVRTQEPTQQHFSVAQ
+sp|Q9H2R5|KLK15_HUMAN  YE----RGRFNCGASLISPHWVLSAAHCQSR----FMRVRLGEHNLRKRDGPEQLRTTSR
+sp|Q9UKR3|KLK13_HUMAN  LV----QGRLLCGGVLVHPKWVLTAAHCLKE----GLKVYLGKHALGRVEAGEQVREVVH
+sp|P16049|TRY1_GADMO   N-----SGYHFCGGSLVSKDWVVSAAHCYKS----VLRVRLGEHHIRVNEGTEQYISSSS
+sp|Q91041|TRYX_GADMO   N-----SGYHFCGGSLVSKDWVVSAAHCYKS----VLRVRLGEHHIRVNEGTEQFISSSS
+sp|P35031|TRY1_SALSA   N-----SGYHFCGGSLVNENWVVSAAHCYKS----RVEVRLGEHNIKVTEGSEQFISSSR
+sp|P35032|TRY2_SALSA   N-----SGYHFCGGSLVNENWVVSAAHCYQS----RVEVRLGEHNIQVTEGSEQFISSSR
+sp|P35033|TRY3_SALSA   Q-----SGYHFCGGSLISSTWVVSAAHCYKS----RIQVRLGEHNIAVNEGTEQFIDSVK
+sp|Q90627|TRY1_CHICK   N-----SGYHFCGGSLISSQWVLSAAHCYKS----SIQVKLGEYNLAAQDGSEQTISSSK
+sp|P00761|TRYP_PIG     N-----SGSHFCGGSLINSQWVVSAAHCYKS----RIQVRLGEHNIDVLEGNEQFINAAK
+sp|P08426|TRY3_RAT     N-----AGYHFCGGSLINSQWVVSAAHCYKS----RIQVRLGEHNIDVVEGGEQFIDAAK
+sp|P00762|TRY1_RAT     N-----SGYHFCGGSLINDQWVVSAAHCYKS----RIQVRLGEHNINVLEGDEQFINAAK
+sp|P06872|TRY2_CANFA   N-----AGYHFCGGSLISDQWVVSAAHCYKS----RIQVRLGEYNIDVLEGNEQFINSAK
+sp|P07477|TRY1_HUMAN   N-----SGYHFCGGSLINEQWVVSAGHCYKS----RIQVRLGEHNIEVLEGNEQFINAAK
+sp|P70059|TRY2_XENLA   N-----AGYHFCGGSLINSQWVVSAAHCYKS----RIQVRLGEHNIALNEGTEQFIDSQK
+                                  *.. *:   :*::*.**        : * ** :     :   :      
+
+sp|P00746|CFAD_HUMAN   AVPHPDSQPD----TIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGI
+sp|P51779|CFAD_PIG     AVPHPDSQPD----TIDHDLLLLKLSEKAELGPAVQPLAWQREDHEVPAGTLCDVAGWGV
+sp|P15119|MCPT2_MOUSE  TFVHPKFQYL----SGFYDIMLLKLQKKAELNSDVDVISLPSSSDFIKPGKMCWTAGWGK
+sp|Q00356|MCPTX_MOUSE  YILPPNYNVS----SKFNDIVLLKLKKQANLTSAVDVVPLPGPSDFAKPGTMCWAAGWGR
+sp|P21844|MCPT5_MOUSE  QFLHPKYDEN----LVVHDIMLLKLKEKAKLTLGVGTLPLSANFNFIPPGRMCRAVGWGR
+sp|P50339|MCPT3_RAT    QFIHPNYDKR----LVLHDIMLLKLKEKAKLTLGVGTLPLSANFNFIPPGRMCRAVGWGR
+sp|P50341|MCPT2_MERUN  QFPHPKYDDY----SVLHDIMLLKLKEKAKLTLAVGTLPLPAKFSFIPPGRVCRAVGWGK
+sp|P24158|PRTN3_HUMAN  VFLN-NYDAE----NKLNDVLLIQLSSPANLSASVATVQLPQQDQPVPHGTQCLAMGWGR
+sp|Q9H2R5|KLK15_HUMAN  VIPHPRYEAR----SHRNDIMLLRLVQPARLNPQVRPAVLPTR--CPHPGEACVVSGWGL
+sp|Q9UKR3|KLK13_HUMAN  SIPHPEYRRSPTHLNHDHDIMLLELQSPVQLTGYIQTLPLSHN-NRLTPGTTCRVSGWGT
+sp|P16049|TRY1_GADMO   VIRHPNYSSY----NINNDIMLIKLTKPATLNQYVHAVALPTE--CAADATMCTVSGWGN
+sp|Q91041|TRYX_GADMO   VIRHPNYSSY----NIDNDIMLIKLTEPATLNQYVHAVALPTE--CAADATMCTVSGWGN
+sp|P35031|TRY1_SALSA   VIRHPNYSSY----NIDNDIMLIKLSKPATLNTYVQPVALPTS--CAPAGTMCTVSGWGN
+sp|P35032|TRY2_SALSA   VIRHPNYSSY----NIDNDIMLIKLSKPATLNTYVQPVALPTS--CAPAGTMCTVSGWGN
+sp|P35033|TRY3_SALSA   VIMHPSYNSR----NLDNDIMLIKLSKPASLNSYVSTVALPSS--CASSGTRCLVSGWGN
+sp|Q90627|TRY1_CHICK   VIRHSGYNAN----TLNNDIMLIKLSKAATLNSYVNTVPLPTS--CVTAGTTCLISGWGN
+sp|P00761|TRYP_PIG     IITHPNFNGN----TLDNDIMLIKLSSPATLNSRVATVSLPRS--CAAAGTECLISGWGN
+sp|P08426|TRY3_RAT     IIRHPSYNAN----TFDNDIMLIKLNSPATLNSRVSTVSLPRS--CGSSGTKCLVSGWGN
+sp|P00762|TRY1_RAT     IIKHPNYSSW----TLNNDIMLIKLSSPVKLNARVAPVALPSA--CAPAGTQCLISGWGN
+sp|P06872|TRY2_CANFA   VIRHPNYNSW----ILDNDIMLIKLSSPAVLNARVATISLPRA--CAAPGTQCLISGWGN
+sp|P07477|TRY1_HUMAN   IIRHPQYDRK----TLNNDIMLIKLSSRAVINARVSTISLPTA--PPATGTKCLISGWGN
+sp|P70059|TRY2_XENLA   VIKHPNYNSR----NLDNDIMLIKLSTTARLSANIQSVPLPSA--CASAGTNCLISGWGN
+                        .                *::*:.*   . :   :              .  *   *** 
+
+sp|P00746|CFAD_HUMAN   VNHAGR-----------RPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAE--SNRRD
+sp|P51779|CFAD_PIG     VSHTGR-----------RPDRLQHLLLPVLDRTTCNLRTYHDGTITERMMCAE--SNRRD
+sp|P15119|MCPT2_MOUSE  TGKNNP-----------LSVTLREVELRIMDQEACKDHSDY---DYQLQVCAGSPTTSKS
+sp|Q00356|MCPTX_MOUSE  TGVKKI-----------ISHTLREVELKIVGEKACKIFRHY---KDSLQICVGSSTKVAS
+sp|P21844|MCPT5_MOUSE  TNVNEP-----------ASDTLQEVKMRLQEPQACKHFTSF---RHNSQLCVGNPKKMQN
+sp|P50339|MCPT3_RAT    TNVNEP-----------ASDTLQEVKMRLQEPQSCKHFTSF---QHKSQLCVGNPKKMQN
+sp|P50341|MCPT2_MERUN  TNVNEP-----------TSDTLQEVKMRLLEAEGCKHFTNF---YHSSQLCVGNPKKMQN
+sp|P24158|PRTN3_HUMAN  VGAHDP-----------PAQVLQELNVTVVTF-FC----------RPHNICTFVPRRKAG
+sp|Q9H2R5|KLK15_HUMAN  VSHNEPGTAGSPRSQVSLPDTLHCANISIISDTSCDK--SYPGRLTNTMVCAGAEGRGAE
+sp|Q9UKR3|KLK13_HUMAN  TTS----------PQVNYPKTLQCANIQLRSDEECRQ--VYPGKITDNMLCAGTKEGGKD
+sp|P16049|TRY1_GADMO   TMSSVA-----------DGDKLQCLSLPILSHADCAN--SYPGMITQSMFCAGYLEGGKD
+sp|Q91041|TRYX_GADMO   TMSSVD-----------DGDKLQCLNLPILSHADCAN--SYPGMITQSMFCAGYLEGGKD
+sp|P35031|TRY1_SALSA   TMSSTA-----------DSNKLQCLNIPILSYSDCNN--SYPGMITNAMFCAGYLEGGKD
+sp|P35032|TRY2_SALSA   TMSSTA-----------DKNKLQCLNIPILSYSDCNN--SYPGMITNAMFCAGYLEGGKD
+sp|P35033|TRY3_SALSA   LSG----------SSSNYPDTLRCLDLPILSSSSCNS--AYPGQITSNMFCAGFMEGGKD
+sp|Q90627|TRY1_CHICK   TLS----------SGSLYPDVLQCLNAPVLSSSQCSS--AYPGRITSNMICIGYLNGGKD
+sp|P00761|TRYP_PIG     TKS----------SGSSYPSLLQCLKAPVLSDSSCKS--SYPGQITGNMICVGFLEGGKD
+sp|P08426|TRY3_RAT     TLS----------SGTNYPSLLQCLDAPVLSDSSCKS--SYPGKITSNMFCLGFLEGGKD
+sp|P00762|TRY1_RAT     TLS----------NGVNNPDLLQCVDAPVLSQADCEA--AYPGEITSSMICVGFLEGGKD
+sp|P06872|TRY2_CANFA   TLS----------SGTNYPELLQCLDAPILTQAQCEA--SYPGQITENMICAGFLEGGKD
+sp|P07477|TRY1_HUMAN   TAS----------SGADYPDELQCLDAPVLSQAKCEA--SYPGKITSNMFCVGFLEGGKD
+sp|P70059|TRY2_XENLA   TLS----------SGTNYPDLLQCLNAPILTDSQCSN--SYPGEITKNMFCAGFLAGGKD
+                                            *:     :     *              .*         
+
+sp|P00746|CFAD_HUMAN   SCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLA---------
+sp|P51779|CFAD_PIG     SCKGDSGGPLVCGGVAEGVVTSGSRVCGNRKKPGIYTRLASYVAWIDGVMADSAAA----
+sp|P15119|MCPT2_MOUSE  IGQGDSGGPLVCDSVAHGIASSY-----EAKAPAVFTRISYYLPWIYKVLKSK-------
+sp|Q00356|MCPTX_MOUSE  VYMGDSGGPLLCAGVAHGIVSSGR---GNAKPPAIFTRISPHVPWINRVIKGK-------
+sp|P21844|MCPT5_MOUSE  VYKGDSGGPLLCAGIAQGIASYVH---RNAKPPAVFTRISHYRPWINKILREN-------
+sp|P50339|MCPT3_RAT    VYKGDSGGPLLCAGIAQGIASYVH---PNAKPPAVFTRISHYRPWINKILREN-------
+sp|P50341|MCPT2_MERUN  VYKGDSGGPLLCAGIAQGIASYVR---RNARPPAVFTRISHYRPWINKILREN-------
+sp|P24158|PRTN3_HUMAN  ICFGDSGGPLICDGIIQGIDSFVIWGCATRLFPDFFTRVALYVDWIRSTLRRVEAKGR--
+sp|Q9H2R5|KLK15_HUMAN  SCEGDSGGPLVCGGILQGIVSWGDVPCDNTTKPGVYTKVCHYLEWIRETMKR--------
+sp|Q9UKR3|KLK13_HUMAN  SCEGDSGGPLVCNRTLYGIVSWGDFPCGQPDRPGVYTRVSRYVLWIRETIRKYETQQQKW
+sp|P16049|TRY1_GADMO   SCQGDSGGPVVCNGVLQGVVSWG-YGCAERDHPGVYAKVCVLSGWVRDTMANY-------
+sp|Q91041|TRYX_GADMO   SCQGDSGGPVVCNGVLQGVVSWG-YGCAERDNPGVYAKVCVLSGWVRDTMASY-------
+sp|P35031|TRY1_SALSA   SCQGDSGGPVVCNGELQGVVSWG-YGCAEPGNPGVYAKVCIFNDWLTSTMASY-------
+sp|P35032|TRY2_SALSA   SCQGDSGGPVVCNGELQGVVSWG-YGCAEPGNPGVYAKVCIFNDWLTSTMATY-------
+sp|P35033|TRY3_SALSA   SCQGDSGGPVVCNGQLQGVVSWG-YGCAQRNKPGVYTKVCNYRSWISSTMSSN-------
+sp|Q90627|TRY1_CHICK   SCQGDSGGPVVCNGQLQGIVSWG-IGCAQKGYPGVYTKVCNYVSWIKTTMSSN-------
+sp|P00761|TRYP_PIG     SCQGDSGGPVVCNGQLQGIVSWG-YGCAQKNKPGVYTKVCNYVNWIQQTIAAN-------
+sp|P08426|TRY3_RAT     SCQGDSGGPVVCNGQLQGVVSWG-YGCAQKGKPGVYTKVCNYVNWIQQTVAAN-------
+sp|P00762|TRY1_RAT     SCQGDSGGPVVCNGQLQGIVSWG-YGCALPDNPGVYTKVCNFVGWIQDTIAAN-------
+sp|P06872|TRY2_CANFA   SCQGDSGGPVVCNGELQGIVSWG-YGCAQKNKPGVYTKVCNFVDWIQSTIAANS------
+sp|P07477|TRY1_HUMAN   SCQGDSGGPVVCNGQLQGVVSWG-DGCAQKNKPGVYTKVYNYVKWIKNTIAANS------
+sp|P70059|TRY2_XENLA   SCQGDSGGPVVCNGQLQGVVSWG-YGCAQRNYPGVYTKVCNFVTWIQSTISSN-------
+                          ******::*     *: :           * .::::     *:   :          
+
+sp|P00746|CFAD_HUMAN   -----
+sp|P51779|CFAD_PIG     -----
+sp|P15119|MCPT2_MOUSE  -----
+sp|Q00356|MCPTX_MOUSE  -----
+sp|P21844|MCPT5_MOUSE  -----
+sp|P50339|MCPT3_RAT    -----
+sp|P50341|MCPT2_MERUN  -----
+sp|P24158|PRTN3_HUMAN  ----P
+sp|Q9H2R5|KLK15_HUMAN  ----N
+sp|Q9UKR3|KLK13_HUMAN  LKGPQ
+sp|P16049|TRY1_GADMO   -----
+sp|Q91041|TRYX_GADMO   -----
+sp|P35031|TRY1_SALSA   -----
+sp|P35032|TRY2_SALSA   -----
+sp|P35033|TRY3_SALSA   -----
+sp|Q90627|TRY1_CHICK   -----
+sp|P00761|TRYP_PIG     -----
+sp|P08426|TRY3_RAT     -----
+sp|P00762|TRY1_RAT     -----
+sp|P06872|TRY2_CANFA   -----
+sp|P07477|TRY1_HUMAN   -----
+sp|P70059|TRY2_XENLA   -----
+                            
+
+
+