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JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.
[jabaws.git] / binaries / src / tcoffee / example / prf3.fasta
diff --git a/binaries/src/tcoffee/example/prf3.fasta b/binaries/src/tcoffee/example/prf3.fasta
new file mode 100644 (file)
index 0000000..bdef2d8
--- /dev/null
+++ b/binaries/src/tcoffee/example/prf3.fasta
@@ -0,0 +1,130 @@
+
+>sp|Q00356|MCPTX_MOUSE Mast cell protease-like protein precursor (EC 3.4.21.-) - Mus musculus (Mouse).
+MQALLFLMALLLPSGAGAEEIIGGVESEPHSRPYMAYVNTFRRKGYVAICGGFLITPQFV
+MTAAHCRGRRMTVTLGAHNVRKRECTQQKIKVEKYILPPNYNVSSKFNDIVLLKLKKQAN
+LTSAVDVVPLPGPSDFAKPGTMCWAAGWGRTGVKKIISHTLREVELKIVGEKACKIFRHY
+KDSLQICVGSSTKVASVYMGDSGGPLLCAGVAHGIVSSGRGNAKPPAIFTRISPHVPWIN
+RVIKGK
+>sp|P50339|MCPT3_RAT Mast cell protease 3 precursor (EC 3.4.21.-) (Mast cell protease III) (rMCP-III) (rMCP-3) (Chymase 1) - Rattus norvegicus (Rat).
+MNLHALCLLLLLLGSSTKAGEIIGGTECIPHSRPYMAYLEIVTSDNYLSACSGFLIRRNF
+VLTAAHCAGRSITVLLGAHNKTYKEDTWQKLEVEKQFIHPNYDKRLVLHDIMLLKLKEKA
+KLTLGVGTLPLSANFNFIPPGRMCRAVGWGRTNVNEPASDTLQEVKMRLQEPQSCKHFTS
+FQHKSQLCVGNPKKMQNVYKGDSGGPLLCAGIAQGIASYVHPNAKPPAVFTRISHYRPWI
+NKILREN
+>sp|P21844|MCPT5_MOUSE Mast cell protease 5 precursor (EC 3.4.21.-) (MMCP-5) (Mast cell chymase 1) - Mus musculus (Mouse).
+MHLLTLHLLLLLLGSSTKAGEIIGGTECIPHSRPYMAYLEIVTSENYLSACSGFLIRRNF
+VLTAAHCAGRSITVLLGAHNKTSKEDTWQKLEVEKQFLHPKYDENLVVHDIMLLKLKEKA
+KLTLGVGTLPLSANFNFIPPGRMCRAVGWGRTNVNEPASDTLQEVKMRLQEPQACKHFTS
+FRHNSQLCVGNPKKMQNVYKGDSGGPLLCAGIAQGIASYVHRNAKPPAVFTRISHYRPWI
+NKILREN
+>sp|P50341|MCPT2_MERUN Mast cell protease 2 precursor (EC 3.4.21.-) - Meriones unguiculatus (Mongolian jird) (Mongolian gerbil).
+MHLLALHLLLFLLGSRAKAGEIIGGTECKPHSRPYMAYLEIATSKNYLSTCSGFLIRRNF
+VLTAAHCSGRSITVLLGAHNKTAKEDTWQKIEVEKQFPHPKYDDYSVLHDIMLLKLKEKA
+KLTLAVGTLPLPAKFSFIPPGRVCRAVGWGKTNVNEPTSDTLQEVKMRLLEAEGCKHFTN
+FYHSSQLCVGNPKKMQNVYKGDSGGPLLCAGIAQGIASYVRRNARPPAVFTRISHYRPWI
+NKILREN
+>sp|P15119|MCPT2_MOUSE Mast cell protease 2 precursor (EC 3.4.21.-) (MMCP-2) - Mus musculus (Mouse).
+MQALLFLMALLLPSGAGAEEIIGGVEAKPHSRPYMAYLKFTTKNGSKERCGGFLIAPQFV
+MTAAHCNGSEISVILGAHNINKNEPTQQIIKTEKTFVHPKFQYLSGFYDIMLLKLQKKAE
+LNSDVDVISLPSSSDFIKPGKMCWTAGWGKTGKNNPLSVTLREVELRIMDQEACKDHSDY
+DYQLQVCAGSPTTSKSIGQGDSGGPLVCDSVAHGIASSYEAKAPAVFTRISYYLPWIYKV
+LKSK
+>sp|P35033|TRY3_SALSA Trypsin-3 precursor (EC 3.4.21.4) (Trypsin III) (Fragment) - Salmo salar (Atlantic salmon).
+FAVAFAAPIDDEDDKIVGGYECRKNSASYQASLQSGYHFCGGSLISSTWVVSAAHCYKSR
+IQVRLGEHNIAVNEGTEQFIDSVKVIMHPSYNSRNLDNDIMLIKLSKPASLNSYVSTVAL
+PSSCASSGTRCLVSGWGNLSGSSSNYPDTLRCLDLPILSSSSCNSAYPGQITSNMFCAGF
+MEGGKDSCQGDSGGPVVCNGQLQGVVSWGYGCAQRNKPGVYTKVCNYRSWISSTMSSN
+>sp|P70059|TRY2_XENLA Trypsin precursor (EC 3.4.21.4) - Xenopus laevis (African clawed frog).
+MKFLVILVLLGAAVAFEDDDKIVGGFTCAKNAVPYQVSLNAGYHFCGGSLINSQWVVSAA
+HCYKSRIQVRLGEHNIALNEGTEQFIDSQKVIKHPNYNSRNLDNDIMLIKLSTTARLSAN
+IQSVPLPSACASAGTNCLISGWGNTLSSGTNYPDLLQCLNAPILTDSQCSNSYPGEITKN
+MFCAGFLAGGKDSCQGDSGGPVVCNGQLQGVVSWGYGCAQRNYPGVYTKVCNFVTWIQST
+ISSN
+>sp|P35032|TRY2_SALSA Trypsin-2 precursor (EC 3.4.21.4) (Trypsin II) (Fragment) - Salmo salar (Atlantic salmon).
+AAFATEDDKIVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYQSRVEVRLG
+EHNIQVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPTSCAP
+AGTMCTVSGWGNTMSSTADKNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDS
+CQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMATY
+>sp|P00762|TRY1_RAT Anionic trypsin-1 precursor (EC 3.4.21.4) (Anionic trypsin I) (Pretrypsinogen I) - Rattus norvegicus (Rat).
+MSALLILALVGAAVAFPLEDDDKIVGGYTCPEHSVPYQVSLNSGYHFCGGSLINDQWVVS
+AAHCYKSRIQVRLGEHNINVLEGDEQFINAAKIIKHPNYSSWTLNNDIMLIKLSSPVKLN
+ARVAPVALPSACAPAGTQCLISGWGNTLSNGVNNPDLLQCVDAPVLSQADCEAAYPGEIT
+SSMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCALPDNPGVYTKVCNFVGWIQ
+DTIAAN
+>sp|P35031|TRY1_SALSA Trypsin-1 precursor (EC 3.4.21.4) (Trypsin I) - Salmo salar (Atlantic salmon).
+MISLVFVLLIGAAFATEDDKIVGGYECKAYSQTHQVSLNSGYHFCGGSLVNENWVVSAAH
+CYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYV
+QPVALPTSCAPAGTMCTVSGWGNTMSSTADSNKLQCLNIPILSYSDCNNSYPGMITNAMF
+CAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMA
+SY
+>sp|P06872|TRY2_CANFA Anionic trypsin precursor (EC 3.4.21.4) - Canis familiaris (Dog).
+MNPLLILAFLGAAVATPTDDDDKIVGGYTCEENSVPYQVSLNAGYHFCGGSLISDQWVVS
+AAHCYKSRIQVRLGEYNIDVLEGNEQFINSAKVIRHPNYNSWILDNDIMLIKLSSPAVLN
+ARVATISLPRACAAPGTQCLISGWGNTLSSGTNYPELLQCLDAPILTQAQCEASYPGQIT
+ENMICAGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCAQKNKPGVYTKVCNFVDWIQ
+STIAANS
+>sp|P24158|PRTN3_HUMAN Myeloblastin precursor (EC 3.4.21.76) (Leukocyte proteinase 3) (PR-3) (PR3) (AGP7) (Wegener's autoantigen) (P29) (C-ANCA antigen) (Neutrophil proteinase 4) (NP-4) - Homo sapiens (Human).
+MAHRPPSPALASVLLALLLSGAARAAEIVGGHEAQPHSRPYMASLQMRGNPGSHFCGGTL
+IHPSFVLTAAHCLRDIPQRLVNVVLGAHNVRTQEPTQQHFSVAQVFLNNYDAENKLNDVL
+LIQLSSPANLSASVATVQLPQQDQPVPHGTQCLAMGWGRVGAHDPPAQVLQELNVTVVTF
+FCRPHNICTFVPRRKAGICFGDSGGPLICDGIIQGIDSFVIWGCATRLFPDFFTRVALYV
+DWIRSTLRRVEAKGRP
+>sp|P07477|TRY1_HUMAN Trypsin-1 precursor (EC 3.4.21.4) (Trypsin I) (Cationic trypsinogen) - Homo sapiens (Human).
+MNPLLILTFVAAALAAPFDDDDKIVGGYNCEENSVPYQVSLNSGYHFCGGSLINEQWVVS
+AGHCYKSRIQVRLGEHNIEVLEGNEQFINAAKIIRHPQYDRKTLNNDIMLIKLSSRAVIN
+ARVSTISLPTAPPATGTKCLISGWGNTASSGADYPDELQCLDAPVLSQAKCEASYPGKIT
+SNMFCVGFLEGGKDSCQGDSGGPVVCNGQLQGVVSWGDGCAQKNKPGVYTKVYNYVKWIK
+NTIAANS
+>sp|P16049|TRY1_GADMO Trypsin-1 precursor (EC 3.4.21.4) (Trypsin I) - Gadus morhua (Atlantic cod).
+MKSLIFVLLLGAVFAEEDKIVGGYECTKHSQAHQVSLNSGYHFCGGSLVSKDWVVSAAHC
+YKSVLRVRLGEHHIRVNEGTEQYISSSSVIRHPNYSSYNINNDIMLIKLTKPATLNQYVH
+AVALPTECAADATMCTVSGWGNTMSSVADGDKLQCLSLPILSHADCANSYPGMITQSMFC
+AGYLEGGKDSCQGDSGGPVVCNGVLQGVVSWGYGCAERDHPGVYAKVCVLSGWVRDTMAN
+Y
+>sp|Q9UKR3|KLK13_HUMAN Kallikrein-13 precursor (EC 3.4.21.-) (Kallikrein-like protein 4) (KLK-L4) - Homo sapiens (Human).
+MWPLALVIASLTLALSGGVSQESSKVLNTNGTSGFLPGGYTCFPHSQPWQAALLVQGRLL
+CGGVLVHPKWVLTAAHCLKEGLKVYLGKHALGRVEAGEQVREVVHSIPHPEYRRSPTHLN
+HDHDIMLLELQSPVQLTGYIQTLPLSHNNRLTPGTTCRVSGWGTTTSPQVNYPKTLQCAN
+IQLRSDEECRQVYPGKITDNMLCAGTKEGGKDSCEGDSGGPLVCNRTLYGIVSWGDFPCG
+QPDRPGVYTRVSRYVLWIRETIRKYETQQQKWLKGPQ
+>sp|Q91041|TRYX_GADMO Trypsin-10 precursor (EC 3.4.21.4) (Trypsin X) - Gadus morhua (Atlantic cod).
+MKSLIFVLLLGAVFAEEDKIVGGYECTRHSQAHQVSLNSGYHFCGGSLVSKDWVVSAAHC
+YKSVLRVRLGEHHIRVNEGTEQFISSSSVIRHPNYSSYNIDNDIMLIKLTEPATLNQYVH
+AVALPTECAADATMCTVSGWGNTMSSVDDGDKLQCLNLPILSHADCANSYPGMITQSMFC
+AGYLEGGKDSCQGDSGGPVVCNGVLQGVVSWGYGCAERDNPGVYAKVCVLSGWVRDTMAS
+Y
+>sp|Q90627|TRY1_CHICK Trypsin I-P1 precursor (EC 3.4.21.4) - Gallus gallus (Chicken).
+MKFLVLVAFVGVTVAFPISDEDDDKIVGGYSCARSAAPYQVSLNSGYHFCGGSLISSQWV
+LSAAHCYKSSIQVKLGEYNLAAQDGSEQTISSSKVIRHSGYNANTLNNDIMLIKLSKAAT
+LNSYVNTVPLPTSCVTAGTTCLISGWGNTLSSGSLYPDVLQCLNAPVLSSSQCSSAYPGR
+ITSNMICIGYLNGGKDSCQGDSGGPVVCNGQLQGIVSWGIGCAQKGYPGVYTKVCNYVSW
+IKTTMSSN
+>sp|P51779|CFAD_PIG Complement factor D precursor (EC 3.4.21.46) (C3 convertase activator) (Properdin factor D) (Adipsin) - Sus scrofa (Pig).
+MADRSGHLAALILLGAAVCVAQPRGRILGGQEAKSHERPYMASVQVNGKHVCGGFLVSEQ
+WVLSAAHCLEDVAEGKLQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLK
+LSEKAELGPAVQPLAWQREDHEVPAGTLCDVAGWGVVSHTGRRPDRLQHLLLPVLDRTTC
+NLRTYHDGTITERMMCAESNRRDSCKGDSGGPLVCGGVAEGVVTSGSRVCGNRKKPGIYT
+RLASYVAWIDGVMADSAAA
+>sp|P00746|CFAD_HUMAN Complement factor D precursor (EC 3.4.21.46) (C3 convertase activator) (Properdin factor D) (Adipsin) - Homo sapiens (Human).
+MHSSVYFAVLVLLGAAACAARPRGRILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQW
+VLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQL
+SEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCN
+RRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTR
+VASYAAWIDSVLA
+>sp|Q9H2R5|KLK15_HUMAN Kallikrein-15 precursor (EC 3.4.21.-) (ACO protease) - Homo sapiens (Human).
+MWLLLTLSFLLASTAAQDGDKLLEGDECAPHSQPWQVALYERGRFNCGASLISPHWVLSA
+AHCQSRFMRVRLGEHNLRKRDGPEQLRTTSRVIPHPRYEARSHRNDIMLLRLVQPARLNP
+QVRPAVLPTRCPHPGEACVVSGWGLVSHNEPGTAGSPRSQVSLPDTLHCANISIISDTSC
+DKSYPGRLTNTMVCAGAEGRGAESCEGDSGGPLVCGGILQGIVSWGDVPCDNTTKPGVYT
+KVCHYLEWIRETMKRN
+>sp|P00761|TRYP_PIG Trypsin precursor (EC 3.4.21.4) - Sus scrofa (Pig).
+FPTDDDDKIVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGE
+HNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAA
+GTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDS
+CQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN
+>sp|P08426|TRY3_RAT Cationic trypsin-3 precursor (EC 3.4.21.4) (Cationic trypsin III) (Pretrypsinogen III) - Rattus norvegicus (Rat).
+MKALIFLAFLGAAVALPLDDDDDKIVGGYTCQKNSLPYQVSLNAGYHFCGGSLINSQWVV
+SAAHCYKSRIQVRLGEHNIDVVEGGEQFIDAAKIIRHPSYNANTFDNDIMLIKLNSPATL
+NSRVSTVSLPRSCGSSGTKCLVSGWGNTLSSGTNYPSLLQCLDAPVLSDSSCKSSYPGKI
+TSNMFCLGFLEGGKDSCQGDSGGPVVCNGQLQGVVSWGYGCAQKGKPGVYTKVCNYVNWI
+QQTVAAN
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