JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.
[jabaws.git] / binaries / src / tcoffee / example / sproteases_small.cw_aln
diff --git a/binaries/src/tcoffee/example/sproteases_small.cw_aln b/binaries/src/tcoffee/example/sproteases_small.cw_aln
new file mode 100644 (file)
index 0000000..ab0831e
--- /dev/null
@@ -0,0 +1,149 @@
+CLUSTAL W (1.83) multiple sequence alignment
+
+
+sp|P29786|TRY3_AEDAE       -----MNQFLFVSFCALLDSAKVSAATLS-----------------SGRI
+sp|P35037|TRY3_ANOGA       -MISNKIAILLAVLVVAVACAQARVAQQHRSVQALPRFLPRPKYDVGHRI
+sp|P03953|CFAD_MOUSE       -----MHSSVYFVALVILGAAVCAAQPRG-------------------RI
+sp|P20160|CAP7_HUMAN       ----MTRLTVLALLAGLLASSRAGSSPLL-------------------DI
+sp|P80015|CAP7_PIG         -------------------------------------------------I
+sp|P08246|ELNE_HUMAN       -MTLGRRLACLFLACVLPALLLGGTALAS-------------------EI
+sp|Q00871|CTRB1_PENVA      ----MIGKLSLLLVCVAVASGNPAAGKPWHWKSPKPLVDPRIHVNATPRI
+sp|P07338|CTRB1_RAT        ------MAFLWLVSCFALVGATFGCG--------VPTIQP--VLTGLSRI
+sp|P00773|ELA1_RAT         -------MLRFLVFASLVLYGHSTQD----------------FPETNARV
+sp|Q06606|GRZ2_RAT         --------MFLFLFFLVAILPVNTEG---------------------GEI
+sp|P08884|GRAE_MOUSE       --------MPPVLILLTLLLPLGAGA---------------------EEI
+sp|P21844|MCPT5_MOUSE      -------MHLLTLHLLLLLLGSSTKA---------------------GEI
+sp|O35205|GRAK_MOUSE       -------MRFSSWALVSLVAGVYMSSECF-----------------HTEI
+sp|Q7YRZ7|GRAA_BOVIN       -MNIPFPFSFPPAICLLLIPGVFPVS--------------------CEGI
+sp|Q9Y5K2|KLK4_HUMAN       MATAGNPWGWFLG-YLILGVAGSLVS-GS-----------------CSQI
+sp|Q91VE3|KLK7_MOUSE       MG------VWLLS-LITVLLSLALETAGQ-----------------GERI
+sp|Q6H321|KLK2_HORSE       --------MWFLVLCLDLSLGETGALPPI-----------------QSRI
+sp|P00757|KLKB4_MOUSE      --------MWFLILFLALSLGGIDAAPPV-----------------QSQV
+sp|Q03238|GRAM_RAT         ------------LLLLLALKTLWAVGNRF-----------------EAQI
+                                                                            :
+
+sp|P29786|TRY3_AEDAE       VGGFQIDIAEVPHQVSLQRSGR----HFCGGSIISPRWVLTRAHCTTNTD
+sp|P35037|TRY3_ANOGA       VGGFEIDVSETPYQVSLQYFNS----HRCGGSVLNSKWILTAAHCTVNLQ
+sp|P03953|CFAD_MOUSE       LGGQEAAAHARPYMASVQVNGT----HVCGGTLLDEQWVLSAAHCMDGVT
+sp|P20160|CAP7_HUMAN       VGGRKARPRQFPFLASIQNQGR----HFCGGALIHARFVMTAASCFQSQN
+sp|P80015|CAP7_PIG         VGGRRAQPQEFPFLASIQKQGR----PFCAGALVHPRFVLTAASCFRGKN
+sp|P08246|ELNE_HUMAN       VGGRRARPHAWPFMVSLQLRGG----HFCGATLIAPNFVMSAAHCVANVN
+sp|Q00871|CTRB1_PENVA      VGGVEATPHSWPHQAALFIDD----MYFCGGSLISSEWVLTAAHCM---D
+sp|P07338|CTRB1_RAT        VNGEDAIPGSWPWQVSLQDKTG---FHFCGGSLISEDWVVTAAHCG---V
+sp|P00773|ELA1_RAT         VGGAEARRNSWPSQISLQYLSGGSWYHTCGGTLIRRNWVMTAAHCV---S
+sp|Q06606|GRZ2_RAT         IWGTESKPHSRPYMAFIKFYDSNSEPHHCGGFLVAKDIVMTAAHCN----
+sp|P08884|GRAE_MOUSE       IGGHVVKPHSRPYMAFVKSVDIEGNRRYCGGFLVQDDFVLTAAHCR----
+sp|P21844|MCPT5_MOUSE      IGGTECIPHSRPYMAYLEIVTSENYLSACSGFLIRRNFVLTAAHCA----
+sp|O35205|GRAK_MOUSE       IGGREVQPHSRPFMASIQYRS----KHICGGVLIHPQWVLTAAHCYSWFP
+sp|Q7YRZ7|GRAA_BOVIN       IGGNEVAPHTRRYMALIKG------LKLCAGALIKENWVLTAAHCD---L
+sp|Q9Y5K2|KLK4_HUMAN       INGEDCSPHSQPWQAALVMEN----ELFCSGVLVHPQWVLSAAHCF----
+sp|Q91VE3|KLK7_MOUSE       IDGYKCKEGSHPWQVALLKGN----QLHCGGVLVDKYWVLTAAHCK----
+sp|Q6H321|KLK2_HORSE       IGGWECEKHSKPWQVAVYHQG----HFQCGGVLVHPQWVLTAAHCM----
+sp|P00757|KLKB4_MOUSE      D----CE-NSQPWHVAVYRFN----KYQCGGVLLDRNWVLTAAHCY----
+sp|Q03238|GRAM_RAT         IGGREAVPHSRPYMVSLQNTK----SHMCGGVLVHQKWVLTAAHCLS--E
+                                           :           *.. ::    ::: * *     
+
+sp|P29786|TRY3_AEDAE       PA-AYTIRAGSTDRTNGG----IIVKVKSVIPHPQYNGDTYNY-------
+sp|P35037|TRY3_ANOGA       PS-SLAVRLGSSRHASGG----TVVRVARVLEHPNYDDSTIDY-------
+sp|P03953|CFAD_MOUSE       DDDSVQVLLGAHSLSAPEP-YKRWYDVQSVVPHPGSRPDSLED-------
+sp|P20160|CAP7_HUMAN       PG-VSTVVLGAYDLRRRER-QSRQTFSISSMSENGYDPQQNLN-------
+sp|P80015|CAP7_PIG         SG-SASVVLGAYDLRQQE--QSRQTFSIRSISQNGYDPRQNLN-------
+sp|P08246|ELNE_HUMAN       VR-AVRVVLGAHNLSRRE--PTRQVFAVQRIFENGYDPVNLLN-------
+sp|Q00871|CTRB1_PENVA      GAGFVEVVLGAHNIRQNEA-SQVSITSTDFFTHENWNSWLLTN-------
+sp|P07338|CTRB1_RAT        KT-SDVVVAGEFDQGSDEE-NIQVLKIAQVFKNPKFNMFTVRN-------
+sp|P00773|ELA1_RAT         SQMTFRVVVGDHNLSQNDG-TEQYVSVQKIMVHPTWNSNNVAAG------
+sp|Q06606|GRZ2_RAT         -GRNIKVTLGAHNIK-KQ-ENTQVISVVKAKPHENYDRDSH---------
+sp|P08884|GRAE_MOUSE       -NRTMTVTLGAHNIKAKE-ETQQIIPVAKAIPHPDYNATAF---------
+sp|P21844|MCPT5_MOUSE      -GRSITVLLGAHNKTSKE-DTWQKLEVEKQFLHPKYDENLV---------
+sp|O35205|GRAK_MOUSE       RGHSPTVVLGAHSLSKNE-PMKQTFEIKKFIPFSRLQSGSA---------
+sp|Q7YRZ7|GRAA_BOVIN       KGN-PQVILGAHSTSHKE-KLDQVFSIKKAIPYPCFDPQTF---------
+sp|Q9Y5K2|KLK4_HUMAN       -QNSYTIGLGLHSLEADQEPGSQMVEASLSVRHPEYNRPLL---------
+sp|Q91VE3|KLK7_MOUSE       -MGQYQVQLGSDKIG-DQ--SAQKIKATKSFRHPGYSTKTH---------
+sp|Q6H321|KLK2_HORSE       -SDDYQIWLGRHNLSEDE-DTAQFHQVSDSFLDPQFDLSLLKKKYLRPYD
+sp|P00757|KLKB4_MOUSE      -NDKYQVWLGKNNFLEDE-PSDQHRLVSKAIPHPDFNMSLLNEHTPQPED
+sp|Q03238|GRAM_RAT         PLQQLKLVFGLHSLHDPQ-DPGLTFYIKQAIKHPGYNLKYEN--------
+                                 :  *                                        
+
+sp|P29786|TRY3_AEDAE       ----DFSLLELDESIGFSRSIEAIALPD-ASETVADGAMCTVSGWGDTKN
+sp|P35037|TRY3_ANOGA       ----DFSLMELESELTFSDVVQPVSLPD-QDEAVEDGTMTIVSGWGNTQS
+sp|P03953|CFAD_MOUSE       ----DLILFKLSQNASLGPHVRPLPLQY-EDKEVEPGTLCDVAGWGVVTH
+sp|P20160|CAP7_HUMAN       ----DLMLLQLDREANLTSSVTILPLPL-QNATVEAGTRCQVAGWGSQRS
+sp|P80015|CAP7_PIG         ----DVLLLQLDREARLTPSVALVPLPP-QNATVEAGTNCQVAGWGTQRL
+sp|P08246|ELNE_HUMAN       ----DIVILQLNGSATINANVQVAQLPA-QGRRLGNGVQCLAMGWGLLGR
+sp|Q00871|CTRB1_PENVA      ----DIALIRLPSPVSLNSNIKTVKLP---SSDVSVGTTVTPTGWGRPSD
+sp|P07338|CTRB1_RAT        ----DITLLKLATPAQFSETVSAVCLPN-VDDDFPPGTVCATTGWGKTKY
+sp|P00773|ELA1_RAT         ---YDIALLRLAQSVTLNNYVQLAVLPQ-EGTILANNNPCYITGWGRTRT
+sp|Q06606|GRZ2_RAT         --FNDIMLLKLERKAQLNGVVKTIALPR-SQDWVKPGQVCTVAGWG--RL
+sp|P08884|GRAE_MOUSE       --FSDIMLLKLESKAKRTKAVRPLKLPR-PNARVKPGDVCSVAGWGSRSI
+sp|P21844|MCPT5_MOUSE      --VHDIMLLKLKEKAKLTLGVGTLPLSA-NFNFIPPGRMCRAVGWG-RTN
+sp|O35205|GRAK_MOUSE       --SHDIMLIKLRTAAELNKNVQLLHLG--SKNYLRDGTKCQVTGWGTTKP
+sp|Q7YRZ7|GRAA_BOVIN       --EGDLQLLQLEGKATMTKAVGILQLPR-TEDDVKPHTKCHVAGWGSTKK
+sp|Q9Y5K2|KLK4_HUMAN       --ANDLMLIKLDESVSESDTIRSISIAS-QCPTA--GNSCLVSGWGLLAN
+sp|Q91VE3|KLK7_MOUSE       --VNDIMLVRLDEPVKMSSKVEAVQLPE-HCEPP--GTSCTVSGWGTTTS
+sp|Q6H321|KLK2_HORSE       DISHDLMLLRLAQPARITDAVKILDLPT-QEPKL--GSTCYTSGWGLIST
+sp|P00757|KLKB4_MOUSE      DYSNDLMLLRLSKPADITDVVKPITLPT-EEPKL--GSTCLASGWGSTTP
+sp|Q03238|GRAM_RAT         ----DLALLKLDGRVKPSKNVKPLALPRKPRDKPAEGSRCSTAGWG-ITH
+                               *. :..*         :    :                 ***    
+
+sp|P29786|TRY3_AEDAE       VF-EMNTLLRAVNVPSYNQAECAAALV--NVVPVTEQMICAGYAAGGKDS
+sp|P35037|TRY3_ANOGA       AA-ESNAILRAANVPTVNQKECTIAYS--SSGGITDRMLCAGYKRGGKDA
+sp|P03953|CFAD_MOUSE       AG-RRPDVLHQLRVSIMNRTTCNLRTY--HDGVVTINMMCAESNR--RDT
+sp|P20160|CAP7_HUMAN       GG-RLSRFPRFVNVTVTPEDQCRPNN------------VCTGVLTRRGGI
+sp|P80015|CAP7_PIG         RR-LFSRFPRVLNVTVTS-NPCLPRD------------MCIGVFSRRGRI
+sp|P08246|ELNE_HUMAN       NR-GIASVLQELNVTVVT-SLCRRSN------------VCTLVRGRQAGV
+sp|Q00871|CTRB1_PENVA      SASGISDVLRQVNVPVMTNADCDSV-----YGIVGDGVVCIDGTGGK-ST
+sp|P07338|CTRB1_RAT        NALKTPEKLQQAALPIVSEADCKKS-----WGSKITDVMTCAGASGV-SS
+sp|P00773|ELA1_RAT         NG-QLSQTLQQAYLPSVDYSICSSSSY---WGSTVKTTMVCAGGDGVRSG
+sp|Q06606|GRZ2_RAT         ANCTSSNTLQEVNLEVQKGQKCQD----MSEDYNDSIQLCVGNPSEGKAT
+sp|P08884|GRAE_MOUSE       NDTKASARLREAQLVIQEDEECKK----RFRHYTETTEICAGDLKKIKTP
+sp|P21844|MCPT5_MOUSE      VNEPASDTLQEVKMRLQEPQACK-----HFTSFRHNSQLCVGNPKKMQNV
+sp|O35205|GRAK_MOUSE       DLLTASDTLREVTVTIISRKRCNSQSYYNHKPVITKDMICAGDARGQKDS
+sp|Q7YRZ7|GRAA_BOVIN       DACQMSNALREANVTVIDRKICNDAQHYNFNPVIDLSMICAGGRKGEDDS
+sp|Q9Y5K2|KLK4_HUMAN       --GRMPTVLQCVNVSVVSEEVCSK----LYDPLYHPSMFCAGGGQDQKDS
+sp|Q91VE3|KLK7_MOUSE       PDVTFPSDLMCSDVKLISSRECKK----VYKDLLGKTMLCAGIPDSKTNT
+sp|Q6H321|KLK2_HORSE       FTNRGSGTLQCVELRLQSNEKCAR----AYPEKMTEFVLCATHRDDSGSI
+sp|P00757|KLKB4_MOUSE      IKFKYPDDLQCVNLKLLPNEDCDK----AHEMKVTDAMLCAGEMDGGSYT
+sp|Q03238|GRAM_RAT         QRGQLAKSLQELDLRLLDTRMCNNSR--FWNGVLTDSMLCLKAGAKGQAP
+                                        :       *                .           
+
+sp|P29786|TRY3_AEDAE       CQGDSGGPLVSGD----KLVGVVSWG-KGCALPN-LPGVYARVST-VRQW
+sp|P35037|TRY3_ANOGA       CQGDSGGPLVVDG----KLVGVVSWG-FGCAMPG-YPGVYARVAV-VRDW
+sp|P03953|CFAD_MOUSE       CRGDSGSPLVCGD----AVEGVVTWGSRVCGNGK-KPGVYTRVSS-YRMW
+sp|P20160|CAP7_HUMAN       CNGDGGTPLVCEG----LAHGVASFSLGPCGRG---PDFFTRVAL-FRDW
+sp|P80015|CAP7_PIG         SQGDRGTPLVCNG----LAQGVASFLRRRFRRS---SGFFTRVAL-FRNW
+sp|P08246|ELNE_HUMAN       CFGDSGSPLVCNG----LIHGIASFVRGGCASGL-YPDAFAPVAQ-FVNW
+sp|Q00871|CTRB1_PENVA      CNGDSGGPLNLNG----MTYGITSFGSSAGCEKG-YPAAFTRVYY-YLDW
+sp|P07338|CTRB1_RAT        CMGDSGGPLVCQKDGVWTLAGIVSWG-SGVCSTS-TPAVYSRVTA-LMPW
+sp|P00773|ELA1_RAT         CQGDSGGPLHCLVNGQYSVHGVTSFVSSMGCNVSKKPTVFTRVSA-YISW
+sp|Q06606|GRZ2_RAT         GKGDSGGPFVCD----GVAQGIVSYRL-CTGTL---PRVFTRISS-FIPW
+sp|P08884|GRAE_MOUSE       FKGDSGGPLVCD----NKAYGLLAYAK-NRTIS---SGVFTKIVH-FLPW
+sp|P21844|MCPT5_MOUSE      YKGDSGGPLLCA----GIAQGIASYVH-RNAKP---PAVFTRISH-YRPW
+sp|O35205|GRAK_MOUSE       CKGDSGGPLICK----GIFHALVSQGY-KCGIAK-KPGIYTLLTKKYQTW
+sp|Q7YRZ7|GRAA_BOVIN       CEGDSGSPLICD----NVFRGVTSFG--KCGNPQ-KPGIYILLTKKHLNW
+sp|Q9Y5K2|KLK4_HUMAN       CNGDSGGPLICN----GYLQGLVSFGKAPCGQVG-VPGVYTNLCK-FTEW
+sp|Q91VE3|KLK7_MOUSE       CNGDSGGPLVCN----DTLQGLVSWGTYPCGQPN-DPGVYTQVCK-YKRW
+sp|Q6H321|KLK2_HORSE       CLGDSGGALICD----GVFQGITSWGYSECADFN-DNFVFTKVMP-HLKW
+sp|P00757|KLKB4_MOUSE      CEHDSGGPLICD----GILQGITSWGPEPCGEPT-EPSVYTKLIK-FSSW
+sp|Q03238|GRAM_RAT         CKGDSGGPLVCGK---GKVDGILSFSSKNCTDIF-KPTVATAVAP-YSSW
+                              * * .:           .: :                  :      *
+
+sp|P29786|TRY3_AEDAE       IREVSEV-------------------
+sp|P35037|TRY3_ANOGA       VRENSGA-------------------
+sp|P03953|CFAD_MOUSE       IENITNGNMTS---------------
+sp|P20160|CAP7_HUMAN       IDGVL----NNPGPGPA---------
+sp|P80015|CAP7_PIG         IDSVL----NNP-P------------
+sp|P08246|ELNE_HUMAN       IDSIIQRSEDNPCPHPRDPDPASRTH
+sp|Q00871|CTRB1_PENVA      IQQKTGVTP-----------------
+sp|P07338|CTRB1_RAT        VQQILEAN------------------
+sp|P00773|ELA1_RAT         MNNVIAYT------------------
+sp|Q06606|GRZ2_RAT         IQKTMKVLQQS---------------
+sp|P08884|GRAE_MOUSE       ISRNMKLL------------------
+sp|P21844|MCPT5_MOUSE      INKILREN------------------
+sp|O35205|GRAK_MOUSE       IKSKLAPSRAH---------------
+sp|Q7YRZ7|GRAA_BOVIN       IKKTIAGAI-----------------
+sp|Q9Y5K2|KLK4_HUMAN       IEKTVQAS------------------
+sp|Q91VE3|KLK7_MOUSE       VMETMKTHR-----------------
+sp|Q6H321|KLK2_HORSE       IKETIEKNS-----------------
+sp|P00757|KLKB4_MOUSE      IRETMANNP-----------------
+sp|Q03238|GRAM_RAT         IRKVIGRWSPQPLT------------
+                           :