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JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.
[jabaws.git] / binaries / src / tcoffee / example / prf1.aln
diff --git a/binaries/src/tcoffee/example/prf1.aln b/binaries/src/tcoffee/example/prf1.aln
new file mode 100644 (file)
index 0000000..54052b1
--- /dev/null
+++ b/binaries/src/tcoffee/example/prf1.aln
@@ -0,0 +1,79 @@
+CLUSTAL FORMAT for T-COFFEE Version_4.32 [http://www.tcoffee.org], CPU=7.25 sec, SCORE=74, Nseq=13, Len=267 
+
+sp|O46683|MCPT3_SHEEP  M--VLFLLLVALLSPAGEAGKIIGGHEAKPHSRPYMAFLQFKISG-KSYICGGFLVREDF
+sp|P80931|MCT1A_SHEEP  M--VLFLLLVALLSPAGEAGKIIGGHEAKPHSRPYMAFLQIKISG-KSYRCGGFLVHEDF
+sp|P80219|DDN1_BOVIN   ---------------------IIGGHEAKPHSRPYMAFLLFKTSG-KSHICGGFLVREDF
+sp|P04187|GRAB_MOUSE   M-KILLLLLTLSLASRTKAGEIIGGHEVKPHSRPYMALLSIKDQQP-EAICGGFLIREDF
+sp|P18291|NKP1_RAT     M-KLLLLLLSFSLAPKTEAGEIIGGHEAKPHSRPYMAYLQIMDEYSGSKKCGGFLIREDF
+sp|Q06605|GRZ1_RAT     M-NLLLLLLTVSLAPTTEAAEIIGGHEADPHSRPYMAYLQYKNEDSRDTICGGFLIREDF
+sp|P10144|GRAB_HUMAN   M-QPILLLLAFLLLPRADAGEIIGGHEAKPHSRPYMAYLMIWDQKS-LKRCGGFLIQDDF
+sp|P20718|GRAH_HUMAN   M-QPFLLLLAFLLTPGAGTEEIIGGHEAKPHSRPYMAFVQFLQEKS-RKRCGGILVRKDF
+sp|P43430|MCPT8_MOUSE  M-FLLLVLLVAALPVNAEGGEIIWGTESKPHSRPYMAYIRFNDSKS-VYRCGGFLVARDI
+sp|P08311|CATG_HUMAN   M-QPLLLLLAFLLPTGAEAGEIIGGRESRPHSRPYMAYLQIQSPAG-QSRCGGFLVREDF
+sp|P28293|CATG_MOUSE   M-QPLLLLLTFILLQGDEAGKIIGGREARPHSYPYMAFLLIQSPEG-LSACGGFLVREDF
+sp|P21812|MCPT4_MOUSE  M-QALLFLMALLLPSGAGAEEIIGGVESRPHSRPYMAHLEITTERGFTATCGGFLITRQF
+sp|P23946|MCPT1_HUMAN  MLLLPLPLLLFLLCSRAEAGEIIGGTECKPHSRPYMAYLEIVTSNGPSKFCGGFLIRRNF
+                                            ** * *  *** **** :           ***:*:  ::
+
+sp|O46683|MCPT3_SHEEP  VLTAAHCLGSSINVTLGAHTITDQERTQQVIQVRRAIPHPDYNDETCANDIMLLQLTRKA
+sp|P80931|MCT1A_SHEEP  VLTAAHCLGSSISVTLGAHNIVDRERTQQVIQVRRAIPHPHYNDKTLANDIMLLQLTRKA
+sp|P80219|DDN1_BOVIN   VLTAAHCLGS-INVTLGAHNIMERERTQQVIPVRRPIPHPDYNDETLANDIMLLKLTRKA
+sp|P04187|GRAB_MOUSE   VLTAAHCEGSIINVTLGAHNIKEQEKTQQVIPMVKCIPHPDYNPKTFSNDIMLLKLKSKA
+sp|P18291|NKP1_RAT     VLTAAHCSGSKINVTLGAHNIKEQEKMQQIIPVVKIIPHPAYNSKTISNDIMLLKLKSKA
+sp|Q06605|GRZ1_RAT     VLTAAHCSGSKINVTLGAHNIKEQEKTQQVIPVVKIIPHPAYNAKTISNDIMLLKLKSKA
+sp|P10144|GRAB_HUMAN   VLTAAHCWGSSINVTLGAHNIKEQEPTQQFIPVKRPIPHPAYNPKNFSNDIMLLQLERKA
+sp|P20718|GRAH_HUMAN   VLTAAHCQGSSINVTLGAHNIKEQERTQQFIPVKRPIPHPAYNPKNFSNDIMLLQLERKA
+sp|P43430|MCPT8_MOUSE  VMTAAHCNGKVINVTLGIHNLKKKKNTQ-LIPVSEAIPHESFDNETLVNDIMLLKLERKA
+sp|P08311|CATG_HUMAN   VLTAAHCWGSNINVTLGAHNIQRRENTQQHITARRAIRHPQYNQRTIQNDIMLLQLSRRV
+sp|P28293|CATG_MOUSE   VLTAAHCLGSSINVTLGAHNIQMRERTQQLITVLRAIRHPDYNPQNIRNDIMLLQLRRRA
+sp|P21812|MCPT4_MOUSE  VMTAAHCSGREITVTLGAHDVSKTESTQQKIKVEKQIVHPKYNFYSNLHDIMLLKLQKKA
+sp|P23946|MCPT1_HUMAN  VLTAAHCAGRSITVTLGAHNITEEEDTWQKLEVIKQFRHPKYNTSTLHHDIMLLKLKEKA
+                       *:***** *  *.**** * :   :     :   . : *  ::  .  :*****:*  :.
+
+sp|O46683|MCPT3_SHEEP  EMTDAVSLINLPRSLEKVKPGMMCSVAGWGQLGVNMPSADKLQEVDLEVQREEKCIARFK
+sp|P80931|MCT1A_SHEEP  EMSDAVSPINLPRSLEKVKPGMMCSVAGWGQLGVNMPSADKLQEVNLEVQSEEECIARFK
+sp|P80219|DDN1_BOVIN   DITDKVSPINLPRSLAEVKPGMMCSVAGWGRLGVNMPSTDKLQEVDLEVQSEEKCIARFK
+sp|P04187|GRAB_MOUSE   KRTRAVRPLNLPRRNVNVKPGDVCYVAGWGRMAPMGKYSNTLQEVELTVQKDRECESYFK
+sp|P18291|NKP1_RAT     KRSSAVKPLNLPRRNVKVKPGDVCYVAGWGKLGPMGKYSDTLQEVELTVQEDQKCESYLK
+sp|Q06605|GRZ1_RAT     KRTRAVKTLSLPRSNFKVKPGDVCYVAGWGKLGPMGKFPDKLQEVELTVQEDQECETYLK
+sp|P10144|GRAB_HUMAN   KRTRAVQPLRLPSNKAQVKPGQTCSVAGWGQTAPLGKHSHTLQEVKMTVQEDRKCESDLR
+sp|P20718|GRAH_HUMAN   KWTTAVRPLRLPSSKAQVKPGQLCSVAGWGYVS-MSTLATTLQEVLLTVQKDCQCERLFH
+sp|P43430|MCPT8_MOUSE  QLNSAVDTIALPKSKDWVKPGQVCTVAGWGKLANC-TLSDTLQEVNLEVQKGQKCRSMSQ
+sp|P08311|CATG_HUMAN   RRNRNVNPVALPRAQEGLRPGTLCTVAGWGRVSMRR-GTDTLREVQLRVQRDRQCLRIFG
+sp|P28293|CATG_MOUSE   RRSGSVKPVALPQASKKLQPGDLCTVAGWGRVSQSR-GTNVLQEVQLRVQMDQMCANRFQ
+sp|P21812|MCPT4_MOUSE  KETPSVNVIPLPRPSDFIKPGKMCRAAGWGRTGVTEPTSDTLREVKLRIMDKEACKN-YW
+sp|P23946|MCPT1_HUMAN  SLTLAVGTLPFPSQFNFVPPGRMCRVAGWGRTGVLKPGSDTLQEVKLRLMDPQACSH-FR
+                         .  *  : :*     : **  * .****  .     .  *:** : :     *     
+
+sp|O46683|MCPT3_SHEEP  D-YIPVTQICAGDPSKRKDSFLGDSGGPLVCDGVAQGIVSYGKDDGTTPNVYTRISSFLS
+sp|P80931|MCT1A_SHEEP  N-YIPITQICAGDSTKRKNSFSGDSGGPLVCNGVAQGIVSYGKDDGTTPDVYTRISSFLS
+sp|P80219|DDN1_BOVIN   N-YIPFTQICAGDPSKRRNSFSGDSGGPLVCNGVAQGIVSYGKNDGTTPDVYTRISSFLP
+sp|P04187|GRAB_MOUSE   NRYNKTNQICAGDPKTKRASFRGDSGGPLVCKKVAAGIVSYGYKDGSPPRAFTKVSSFLS
+sp|P18291|NKP1_RAT     NYFDKANEICAGDPKIKRASFRGDSGGPLVCKKVAAGIVSYGQNDGSTPRAFTKVSTFLS
+sp|Q06605|GRZ1_RAT     NAYDKANQICAGDPKIKCASFQGDSGGPLVCKKVAAGIVSYGRKDGSTPRAFTKVSTFLS
+sp|P10144|GRAB_HUMAN   HYYDSTIELCVGDPEIKKTSFKGDSGGPLVCNKVAQGIVSYGRNNGMPPRACTKVSSFVH
+sp|P20718|GRAH_HUMAN   GNYSRATEICVGDPKKTQTGFKGDSGGPLVCKDVAQGILSYGNKKGTPPGVYIKVSHFLP
+sp|P43430|MCPT8_MOUSE  T-YNDSIQLCVGNPSENKATGKGDSGGPFVCNGVVQGIVSCRLCTGTLPRVFTRISSFMP
+sp|P08311|CATG_HUMAN   -SYDPRRQICVGDRRERKAAFKGDSGGPLLCNNVAHGIVSYGKSSGVPPEVFTRVSSFLP
+sp|P28293|CATG_MOUSE   -FYNSQTQICVGNPRERKSAFRGDSGGPLVCSNVAQGIVSYGSNNGNPPAVFTKIQSFMP
+sp|P21812|MCPT4_MOUSE  -HYDYNLQVCVGSPRKKRSAYKGDSGGPLLCAGVAHGIVSYGRGDAKPPAVFTRISSYVP
+sp|P23946|MCPT1_HUMAN  -DFDHNLQLCVGNPRKTKSAFKGDSGGPLLCAGVAQGIVSYGRSDAKPPAVFTRISHYRP
+                         :    ::*.*.         ******::*  *. **:*     .  * .  ::. :  
+
+sp|O46683|MCPT3_SHEEP  WIQRTMRQY--------KNQGS--A--
+sp|P80931|MCT1A_SHEEP  WIQRTMRRY------------------
+sp|P80219|DDN1_BOVIN   WIKRVMYLF--------K---------
+sp|P04187|GRAB_MOUSE   WIKKTMKSS------------------
+sp|P18291|NKP1_RAT     WIKKTMKKS------------------
+sp|Q06605|GRZ1_RAT     WIEETMKKS------------------
+sp|P10144|GRAB_HUMAN   WIKKTMKRY------------------
+sp|P20718|GRAH_HUMAN   WIKRTMKRL------------------
+sp|P43430|MCPT8_MOUSE  WIRKTMKLL--------Q---Q--P--
+sp|P08311|CATG_HUMAN   WIRTTMRSF--------KLLDQMETPL
+sp|P28293|CATG_MOUSE   WIKRTMRRFAPRYQRPANSLSQAQT--
+sp|P21812|MCPT4_MOUSE  WINRVIKGE------------------
+sp|P23946|MCPT1_HUMAN  WINQILQAN------------------
+                       **.  :                     
+
+
+