--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Nov 25 19:19:30 WET 2016 codeml.models=0 1 2 3 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=CLUSTALW2 tcoffee.params= tcoffee.maxSeqs=0 codeml.bin=codeml mrbayes.tburnin=2500 codeml.dir= input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb_adops tcoffee.bin=t_coffee_ADOPS mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta=/opt/ADOPS/1/5-HT2B-PD/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/1/5-HT2B-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/5-HT2B-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Use the harmonic mean for Bayes factor comparisons of models) (Values are saved to the file /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -10149.24 -10165.35 2 -10149.34 -10162.98 -------------------------------------- TOTAL -10149.29 -10164.75 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/1/5-HT2B-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/5-HT2B-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": Summaries are based on a total of 3002 samples from 2 runs. Each run produced 2001 samples of which 1501 samples were included. Parameter summaries saved to file "/opt/ADOPS/1/5-HT2B-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.199774 0.003742 1.087269 1.321579 1.197929 1194.60 1328.44 1.000 r(A<->C){all} 0.138636 0.000176 0.112819 0.164444 0.138576 861.03 865.95 1.000 r(A<->G){all} 0.246475 0.000349 0.213127 0.286042 0.245706 830.03 844.69 1.000 r(A<->T){all} 0.110364 0.000270 0.080480 0.143740 0.109742 1022.22 1132.50 1.000 r(C<->G){all} 0.087606 0.000078 0.070401 0.104954 0.087431 947.22 1090.00 1.001 r(C<->T){all} 0.350334 0.000472 0.307804 0.391621 0.350381 486.88 622.63 1.000 r(G<->T){all} 0.066586 0.000101 0.046879 0.085910 0.066317 1261.18 1271.07 1.000 pi(A){all} 0.201063 0.000052 0.185712 0.214186 0.200978 805.21 939.62 1.000 pi(C){all} 0.332233 0.000067 0.316525 0.348250 0.332180 834.77 999.71 1.000 pi(G){all} 0.290254 0.000063 0.274461 0.305113 0.290029 1176.83 1229.33 1.000 pi(T){all} 0.176450 0.000040 0.165108 0.189705 0.176345 1040.86 1130.52 1.000 alpha{1,2} 0.150961 0.000112 0.130228 0.170175 0.150427 1090.37 1260.47 1.000 alpha{3} 4.342859 0.919051 2.595539 6.188954 4.242116 1397.20 1449.10 1.000 pinvar{all} 0.375369 0.000622 0.325801 0.423187 0.376214 1008.85 1153.83 1.000 ------------------------------------------------------------------------------------------------------ * Convergence diagnostic (ESS = Estimated Sample Size); min and avg values correspond to minimal and average ESS among runs. ESS value below 100 may indicate that the parameter is undersampled. + Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman and Rubin, 1992) should approach 1.0 as runs converge. Setting sumt conformat to Simple --- CODEML SUMMARY Model 1: NearlyNeutral -8973.005454 Model 2: PositiveSelection -8970.573134 Model 0: one-ratio -9223.752558 Model 3: discrete -8956.695823 Model 7: beta -8964.133518 Model 8: beta&w>1 -8956.584822 Model 0 vs 1 501.49420800000007 Model 2 vs 1 4.864639999999781 Model 8 vs 7 15.097391999999672 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: D_melanogaster_5-HT2B-PD) Pr(w>1) post mean +- SE for w 34 T 0.554 1.897 36 A 0.791 2.473 532 S 0.995** 2.967 643 P 0.996** 2.971 646 V 0.787 2.464 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: D_melanogaster_5-HT2B-PD) Pr(w>1) post mean +- SE for w 21 S 0.862 1.383 +- 0.301 32 D 0.550 1.059 +- 0.506 34 T 0.934 1.446 +- 0.210 36 A 0.954* 1.463 +- 0.178 40 S 0.815 1.332 +- 0.364 46 H 0.650 1.166 +- 0.471 54 G 0.749 1.274 +- 0.401 55 N 0.794 1.312 +- 0.381 373 L 0.732 1.238 +- 0.449 479 K 0.609 1.071 +- 0.559 532 S 0.993** 1.496 +- 0.064 535 T 0.927 1.440 +- 0.221 537 I 0.855 1.377 +- 0.308 550 A 0.815 1.336 +- 0.355 556 A 0.651 1.152 +- 0.494 562 S 0.623 1.139 +- 0.480 620 S 0.593 1.088 +- 0.518 638 P 0.829 1.349 +- 0.343 641 A 0.524 0.968 +- 0.585 642 A 0.803 1.312 +- 0.393 643 P 0.992** 1.494 +- 0.071 646 V 0.955* 1.463 +- 0.177
>C1 MEEDVYASLGAYNDSGGDDWSSSEHLVLWEEDETQRTTANATSRHNQLHV ARWNATGNATISATFEDVPFDANNYWALLALVLVLGTAAGNILVCLAIAW ERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLGSEHCLTWI CLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTLKIVFVWLL SIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFYIPLGVMLL TYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALERRCTWRRLL KPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPTPTTMTALH QFGAEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQLQYPSSPQRYAAT HQQSHHHNHQQHPAGVYHQQASPKGRHGTTVLGLSTTTLGIERESTRNSL ASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVPGREKRAGHEDADEDV ETPTSTLRRHKRHNSLPKNALYPRHTTVQESLDDDDDEEEESAQQKDQQT KSKICHSDTELDPPQKAKQCHIAGQNHQSDYLQLPSVCTCPYFGDRPLQN CVKSAEVKIISSAFRVTTTTTAVSSSPSEMELLMCSSGNKKSLTSSVSAG ITGGPAGAAPATVGSTLSPHSAHNQGSSLTVQSDGSGYLAAPGTPCPGRR KLSISKTASVVTWDSSRHRRRGSSFGGVRTSLLLTPTKTATTSNSSTPLR RSATLRSHQNMNYQGAGECGGKTRTTTSSPCMLQRQQTVRSHHSRNSSVI SRNSSRHGRIIRLEQKATKVLGVVFFTFVILWSPFFVLNLLPTVCAECEE RISHWVFDVVTWLGYASSMVNPIFYTIFNKVFRQAFKKVLLCRYSSTSAW RPSRooooooooooooo >C2 MEEDVYASLGAYNDSGGDDWSSSEHLVLWEEDEAQRPAANATSRHNQLQV ARWNATGNATISATFEDVPFDANNYWALLALVLVLGTAAGNILVCLAIAW ERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLGSEHCLTWI CLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTLKIVFVWLL SIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFYIPLGVMLL TYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALERRCTWRRLL KPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPTPTTMTALH QFGAEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQLQYPSSPQRYAAS HQQSHHHNHQQHPAGVYHQQASPKGRHGTTVLGLSTTTLGIERESTRNSL ASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVPGRDQRAGHEDADEDV DTPTSTLRRHKRHNSLPKNALYPRHTTVQESLDDDDDDEEEERAQQKDQQ TKSKICHSDTELDPPQKSKQCHIAGQNHQSDYLQLPSVCTCPYFGDRPLQ NCVKSAEVKIISSAFRVTTTTTAVSSSPSEMELLMCSSGNKKSLTSSVSA GMTGGPAGAAPATVGSTLSPHSAHNQGSSLTVQSDGSGYLAAPGTPCPGR RKLSISKTASVVTWDSSRHRRRGSSFGGVRTSLLLTPTKTATTSNSSTPL RRSATLRSHQNMNYQGAGECGGKTRTTTSSPCMLQRQQTVRSHHSRNSSV ISRNSSRHGRIIRLEQKATKVLGVVFFTFVILWSPFFVLNLLPTVCAECE ERISHWVFDVVTWLGYASSMVNPIFYTIFNKVFRQAFKKVLLCRYSSTSA WRPSRoooooooooooo >C3 MEEDVYASLGAYNDSGGEDWTSSEHLVLWEEDEAQRVTVNASNRHNHLHV ARWNASGNASITANFEDVPFDANNYWALLALVLVLGTAAGNILVCLAIAW ERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLGSEHCLTWI CLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTLKIVFVWLL SIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFYIPLGVMLL TYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALERRCTWRRLL KPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPTPTTMTALH QFGAEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQLQYPSSPQRYATH QQTHHQHHQHQHNHQQHPAGVYHQQASPKGRHGTTVLGLSTTTLGIERES TRNSLASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVPGRDRRSGHED ADEDVDTPTSTLRRHKRHNSLPKNALYPRHTTVQESLDDDDDDEEEESPQ QKEKQAKPKGCHSDTELDPPQKAKQCHIAGQNHQTDYLQLPSVCTCPYFG DRPLQNCVKSAEVKIISSAFRVTTTTTAVSSSPSEMELLMCSGGNKKSLT SSVSAGTTGGPAGAASAAVGSTLSPHSAHNQGSSLTVQSDGSGYLAAPGT PCPGRRKLSISKTASVVTWDSSRHRRRGSSFGGVRTSLLLTPTKTATAFN SSTPLRRSATLRSHQNMNYQGAGDCGSKTRTTTSSPCMLQRQQTVRSHHS RNSSVISRNSSRHGRIIRLEQKATKVLGVVFFTFVILWSPFFVLNLLPTV CAECEERISHWVFDVVTWLGYASSMVNPIFYTIFNKVFRQAFKKVLLCRY SSTSAWRPSRooooooo >C4 MEEDVYASLGAYNDSGGVDWSSSEHLVLWEEDEAQRAAVNASNRHNQLQM GRLNATGNASITATFEDAPFDANNYWALLALVLVLGTAAGNILVCLAIAW ERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLGSEHCLTWI CLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTLKIVFVWLL SIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFYIPLGVMLL TYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALERRCTWRRLL KPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPTPTTMTALH QFGAEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQLQYPSSPQRYATH QQTHQQSHHQQHHNHQQHPGGAYHQQASPKGRHGATTLGLSTTTLGIERE STRNSLASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVPGRDRRSGHE DADEDVDTPTSTLRRHKRHNSLPKNALYQRHTTVQESLDDDDEEEEESPQ QKDQQAKTKICHSDTELDPPQKAKQCHIAGQNHQSDYLQLPSVCTCPYFG DRPLQNCVKSAEVKIISSAFRVTTTTTAVSSSPSEMELLMCSSGNKKSMT SSVSAGTTGGPAGAGPATGGSTLSPNSAHNQGSSLTVQSDGSGYLAAPGT PCPGRRKLSISKTASVVTWDSSRHRRRGSSFGGVRTSLLLTPTKTATAFN SSTPLRRSATLRSHQNMNYQGAGDCGAKTRTTTSSPCMLQRQQTVRSHHS RNSSVISRNSSRHGRIIRLEQKATKVLGVVFFTFVILWSPFFVLNLLPTV CAECEERISHWVFDVVTWLGYASSMVNPIFYTIFNKVFRQAFKKVLLCRY SSTSAWRPSRooooooo >C5 MEEDVYASLGAYNDSGGEDWSSSEHLVLWEAEEERGVGANATSRHNQLLL ARWNITNNGTLHAEDVPFDANNYWALLALVLVLGTAAGNILVCLAIAWER RLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLGSEHCLTWICL DVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTLKIVFVWLLSI AMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFYIPLGVMLLTY CLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALERRCTWRRLLKP GPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPTPTTMTALHQF GAEMLKLSRGLESVASSSTTGSPTKSEFSISNHLQLQYPSSPQRYASHHQ QQSHQQQHNHQQHPGNVYHQQTSPKGRQGAAVLGLSTTTLGIERESTRNS LASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVPGRDRRSGHEDADED LDDTPTSTLRRHKRHNSLPKNALYPRHTTVQESLDDDDDDVDGGEEDLKE QQTKFCHSDTELDPPQKTGKQCHIGGQNHQSDYLQLPSVCTCPYFGDRPL QNCVKTAEVKIISSAFRVTTTTTTAVSSSPSEMELLMCTGGGTKKSLTSS VSAGMTGGPGGGGPPPATVGSTLSPHSAHNQGSSLTVQSDGSGYLAAPGT PCPGRRKLSISKTASVVTWDSSRHRRRGSSFGGVRTSLLLTPTKTATAST ASSTPLRRSATLRSHQNMNYQGQGDCGAGKTRTTTSSPCMLQRQQTVRSH HSRNSSVISRNSSRHGRIIRLEQKATKVLGVVFFTFVILWSPFFVLNLLP TVCAECEERISHWVFDVVTWLGYASSMVNPIFYTIFNKVFRQAFKKVLLC RYSSTSAWRPSRooooo >C6 MEEDVYASLGAYNDSGGEDWTSSEHLVLWEETEVEPAGGNASSRHNQLLL ASWNISGNVTSTEDVPFDANNYWALLALVLVLGTAAGNILVCLAIAWERR LQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLGSEHCLTWICLD VLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTLKIVFVWLLSIA MSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFYIPLGVMLLTYC LTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALERRCTWRRLLKPG PGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPTPTTMTALHQFG AEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQMQFPSSPQRYATHLQQ SHQQQHNHQPYPGSVYHQQVSPKGRQGTTALGMSTTTLGIERESTRNSLA SSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVPGRDRRSGHEDADEDLD TPTSTLRRHKRHNSLPKNALYPRHTTVQESLDDDDDEDEEVSSRNKDQQD HKTKGCHSDTELDPPQKAKQCHIAGQNHQTDYLQLPSVCTCPYFGDRPLQ NCVKTAEVKIVSSAFRVTTTTTTAVSSSPSEMELLMCSGGNKKSLTSSVS AGMTGGGSAAGGAGPPATIGSTLSPHSVHNQGSSLTVQSDSSGYLAAPGT PCPGRRKLSISKTASVVTWDSSRHRRRGSSFGGVRTSLLLTPTKTATPTT SSTPLRRSATLRSHQNMNYQGAGDCGGKTRNTTSSPCMLQRQQTVRSHHS RNSSVISRNSSRHGRIIRLEQKATKVLGVVFFTFVILWSPFFVLNLLPTV CAECEERISHWVFDVVTWLGYASSMVNPIFYTIFNKVFRQAFKKVLLCRY SSTSAWRPSRooooooo >C7 MEEDVYASLGAYNDSGGEEDWASSEHLVLWGEELSGENASNRHNQLQLAR WNVSNATIMEDVPFDANNYWALLALVLVLGTAAGNILVCLAIAWERRLQN VTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLGSEHCLTWICLDVLF CTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTLKIVFVWLLSIAMSL PLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFYIPLGVMLLTYCLTV RLLARQRQNLGGGQQTAAATPGWASGWLGQAPALERRCTWRRLLKPGPGN ASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPTPTTMTALHQFGAEM LKLSRGLESVASSSTTGSPTKSEFSISNHLQLQYPSSPQRYASHQQQQPS HQQHHNHQQHPGSVYHQQTSPKGRHGTTVLGLSTTTLGIERESTRNSLAS SRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVPGRDRRSGHEDADEDLDT PTSTLRRHKRHNSLPKNALYPRHTTVQESLDDDDDDEEEKDQQGNTKFCH SDTELDPPQKPKQCHIAGQNHQTDYLQLPSVCTCPYFGDRPLQNCVKTAE VKIISSAFRVTTTTTAVSSSPSEMELLMCSGGNKKSLTSSVSAGMTGGSA GGGGPPPTGGSTLSPHSAHNQGSSLTVQSDGSGYLAAPGTPCPGRRKLSI SKTASVVTWDSSRHRRRGSSFGGVRTSLLLTPTKTATPSTSSTPLRRSAT LRSHQNMNYQGAGDCGGKTRTTTSSPCMLQRQQTVRSHHSRNSSVISRNS SRHGRIIRLEQKATKVLGVVFFTFVILWSPFFVLNLLPTVCAECEERISH WVFDVVTWLGYASSMVNPIFYTIFNKVFRQAFKKVLLCRYSSTSAWRPSR ooooooooooooooooo >C8 MEEDVYASLGAYNDSGGEDWSSAEHLVLWEEELPGENASQRHHNHLQLAT WNASNGTAPTTTTTTITTLEDVPFDANNYWALLALVLVLGTAAGNILVCL AIAWERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLGSEHC LTWICLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTLKIVF VWLLSIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFYIPLG VMLLTYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALERRCTW RRLLKPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPTPTTM TALHQFGAEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQLQYPSSPQR YATHQQSVPQSHQPHHHHNQPNPGSAYHQQTSPKNRQGTTALGLSTTTLG IERESTRNSLASSRMGEQSDGTLSQLSQRIRAYKKRRRASSAVPGRDRRS GVEDDDGDEDLDTLTSTLRRHKRHNSLPKNALYPRHTTVQESLDDDDEEE EEEVRKEQQSKTKFCHSDTELDPPQNQKQCHIAGQNHQSDYLQLPSVCTC PYFGDRPLQNCVKTAEVKIISSAFRVTTTTTAVSSSPSEMELLMCSAGNK KSLTSSVSAGITGGSSGAGPPQTGGSTLSPHSAQNQGSSLTVQSDGSGFL AAPGTPCPGRRKLSISKTASVVTWDSGRHRRRGSSFGGVRTSLLLTPTKT ATASTSSTPLRRSATLRSHQNMNYQGAGECGGKARTTTSSPCMLQRQQTV RSHHSRNSSVISRNSSRHGRIIRLEQKATKVLGVVFFTFVILWSPFFVLN LLPTVCAECEERISHWVFDVVTWLGYASSMVNPIFYTIFNKVFRQAFKKV LLCRYSSTSAWRPSRoo >C9 MEEDVYASLGAYNDSGGEDWSSAEHLVLWEEDEQERPGGNDSHRHNQLLL SRWNATSGSGNATVIEDVPFDANNYWALLALVLVLGTAAGNILVCLAIAW ERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLGSEHCLTWI CLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTLKIVFVWLL SIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFYIPLGVMLL TYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALERRCTWRRLL KPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPTPTTMTALH QFGAEMLKLSRGLESVASSSTTGSPTKSEFSISNHLQLQYPCSPQRYAPH HASALQPHQPHHHHHHHQQPGGVYHQQTSPKGRQGTTVLGLSTTTLGIER ESTRNSLASSRMGGEQSDGTLSQLSQRLRAYKNRRRASSAVPGRDRRSGH EDADEDLDTPTSTLRRHKRHNSLPKNALYPRHTTLQESLDDDDDEEDERA RHKDSPSKTKICHSDTELDPPQNAKQCHANGQDHQTDYLQLPSVCTCPYF GDRPLQNCVKTAEVKIISSAFRVTTTTTAVSSSPSEMELLMCSGGKKKSL TSSVSAGMTGGSAGGGAGGGGPPATCGSTLSPHSAHNQGSSLTVQSDGSG YLAAPGTPCPGRRKLSISKTASVVTWDSSRHRRRGSSFGGVRTSLLLTPT KTATASTSSTPLRRSATLRSHQNMNYQGAGECGGKARTTTSSPCMLQRQQ TVRSHHSRNSSVISRNSSRHGRIIRLEQKATKVLGVVFFTFVILWSPFFV LNLLPTVCAECEERISHWVFDVVTWLGYASSMVNPIFYTIFNKVFRQAFK KVLLCRYSNTSAWRPSR CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE: ], CPU=0.00 sec, SCORE=100, Nseq=9, Len=952 C1 MEEDVYASLGAYNDSGGD-DWSSSEHLVLWEEDETQRTTANATSR-HNQL C2 MEEDVYASLGAYNDSGGD-DWSSSEHLVLWEEDEAQRPAANATSR-HNQL C3 MEEDVYASLGAYNDSGGE-DWTSSEHLVLWEEDEAQRVTVNASNR-HNHL C4 MEEDVYASLGAYNDSGGV-DWSSSEHLVLWEEDEAQRAAVNASNR-HNQL C5 MEEDVYASLGAYNDSGGE-DWSSSEHLVLWEAEEERGVGANATSR-HNQL C6 MEEDVYASLGAYNDSGGE-DWTSSEHLVLWEETEVEPAGGNASSR-HNQL C7 MEEDVYASLGAYNDSGGEEDWASSEHLVLWGEELS---GENASNR-HNQL C8 MEEDVYASLGAYNDSGGE-DWSSAEHLVLWEEELP---GENASQRHHNHL C9 MEEDVYASLGAYNDSGGE-DWSSAEHLVLWEEDEQERPGGNDSHR-HNQL ***************** **:*:****** * : * **:* C1 HVARWNATGNAT------ISATFEDVPFDANNYWALLALVLVLGTAAGNI C2 QVARWNATGNAT------ISATFEDVPFDANNYWALLALVLVLGTAAGNI C3 HVARWNASGNAS------ITANFEDVPFDANNYWALLALVLVLGTAAGNI C4 QMGRLNATGNAS------ITATFEDAPFDANNYWALLALVLVLGTAAGNI C5 LLARWNITNNGT------LHA--EDVPFDANNYWALLALVLVLGTAAGNI C6 LLASWNISGN---------VTSTEDVPFDANNYWALLALVLVLGTAAGNI C7 QLARWNVSNA----------TIMEDVPFDANNYWALLALVLVLGTAAGNI C8 QLATWNASNGTAPTTTTTTITTLEDVPFDANNYWALLALVLVLGTAAGNI C9 LLSRWNATSGSG------NATVIEDVPFDANNYWALLALVLVLGTAAGNI :. * :. : **.************************ C1 LVCLAIAWERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLG C2 LVCLAIAWERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLG C3 LVCLAIAWERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLG C4 LVCLAIAWERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLG C5 LVCLAIAWERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLG C6 LVCLAIAWERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLG C7 LVCLAIAWERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLG C8 LVCLAIAWERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLG C9 LVCLAIAWERRLQNVTNYFLMSLAITDLMVAVLVMPLGILTLVKGYFPLG ************************************************** C1 SEHCLTWICLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTL C2 SEHCLTWICLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTL C3 SEHCLTWICLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTL C4 SEHCLTWICLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTL C5 SEHCLTWICLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTL C6 SEHCLTWICLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTL C7 SEHCLTWICLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTL C8 SEHCLTWICLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTL C9 SEHCLTWICLDVLFCTASIMHLCTISVDRYLSLRYPMRFGRNKTRRRVTL ************************************************** C1 KIVFVWLLSIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFY C2 KIVFVWLLSIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFY C3 KIVFVWLLSIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFY C4 KIVFVWLLSIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFY C5 KIVFVWLLSIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFY C6 KIVFVWLLSIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFY C7 KIVFVWLLSIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFY C8 KIVFVWLLSIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFY C9 KIVFVWLLSIAMSLPLSLMYSKNHASVLVNGTCQIPDPVYKLVGSIVCFY ************************************************** C1 IPLGVMLLTYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALER C2 IPLGVMLLTYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALER C3 IPLGVMLLTYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALER C4 IPLGVMLLTYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALER C5 IPLGVMLLTYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALER C6 IPLGVMLLTYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALER C7 IPLGVMLLTYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALER C8 IPLGVMLLTYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALER C9 IPLGVMLLTYCLTVRLLARQRQNLGGGQQTAAATPGWASGWLGQAPALER ************************************************** C1 RCTWRRLLKPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPT C2 RCTWRRLLKPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPT C3 RCTWRRLLKPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPT C4 RCTWRRLLKPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPT C5 RCTWRRLLKPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPT C6 RCTWRRLLKPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPT C7 RCTWRRLLKPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPT C8 RCTWRRLLKPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPT C9 RCTWRRLLKPGPGNASSVLHAHSANSTDTDLSTLDNHELWLPDSSIKEPT ************************************************** C1 PTTMTALHQFGAEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQLQYPS C2 PTTMTALHQFGAEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQLQYPS C3 PTTMTALHQFGAEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQLQYPS C4 PTTMTALHQFGAEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQLQYPS C5 PTTMTALHQFGAEMLKLSRGLESVASSSTTGSPTKSEFSISNHLQLQYPS C6 PTTMTALHQFGAEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQMQFPS C7 PTTMTALHQFGAEMLKLSRGLESVASSSTTGSPTKSEFSISNHLQLQYPS C8 PTTMTALHQFGAEMLKLSRGLESVASSSTTGSPTKSEFSLSNHLQLQYPS C9 PTTMTALHQFGAEMLKLSRGLESVASSSTTGSPTKSEFSISNHLQLQYPC ***************************************:*****:*:*. C1 SPQRYAATHQ------QSHHHN-HQQHPAGVYHQQASPKGRHGTTVLGLS C2 SPQRYAASHQ------QSHHHN-HQQHPAGVYHQQASPKGRHGTTVLGLS C3 SPQRYATHQQTHHQ-HHQHQHN-HQQHPAGVYHQQASPKGRHGTTVLGLS C4 SPQRYATHQQTHQQSHHQQHHN-HQQHPGGAYHQQASPKGRHGATTLGLS C5 SPQRYASHHQ---QQSHQQQHN-HQQHPGNVYHQQTSPKGRQGAAVLGLS C6 SPQRYATHLQQS----HQQQHN-HQPYPGSVYHQQVSPKGRQGTTALGMS C7 SPQRYASHQQQQ--PSHQQHHN-HQQHPGSVYHQQTSPKGRHGTTVLGLS C8 SPQRYATHQQSVPQSHQPHHHH-NQPNPGSAYHQQTSPKNRQGTTALGLS C9 SPQRYAPHHASALQPHQPHHHHHHHQQPGGVYHQQTSPKGRQGTTVLGLS ******. : ::*: :: *...****.***.*:*::.**:* C1 TTTLGIERESTRNSLASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVP C2 TTTLGIERESTRNSLASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVP C3 TTTLGIERESTRNSLASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVP C4 TTTLGIERESTRNSLASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVP C5 TTTLGIERESTRNSLASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVP C6 TTTLGIERESTRNSLASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVP C7 TTTLGIERESTRNSLASSRMGGEQSDGTLSQLSQRLRAYKKRRRASSAVP C8 TTTLGIERESTRNSLASSRMG-EQSDGTLSQLSQRIRAYKKRRRASSAVP C9 TTTLGIERESTRNSLASSRMGGEQSDGTLSQLSQRLRAYKNRRRASSAVP ********************* *************:****:********* C1 GREKRAGHED--ADEDVE-TPTSTLRRHKRHNSLPKNALYPRHTTVQESL C2 GRDQRAGHED--ADEDVD-TPTSTLRRHKRHNSLPKNALYPRHTTVQESL C3 GRDRRSGHED--ADEDVD-TPTSTLRRHKRHNSLPKNALYPRHTTVQESL C4 GRDRRSGHED--ADEDVD-TPTSTLRRHKRHNSLPKNALYQRHTTVQESL C5 GRDRRSGHED--ADEDLDDTPTSTLRRHKRHNSLPKNALYPRHTTVQESL C6 GRDRRSGHED--ADEDLD-TPTSTLRRHKRHNSLPKNALYPRHTTVQESL C7 GRDRRSGHED--ADEDLD-TPTSTLRRHKRHNSLPKNALYPRHTTVQESL C8 GRDRRSGVEDDDGDEDLD-TLTSTLRRHKRHNSLPKNALYPRHTTVQESL C9 GRDRRSGHED--ADEDLD-TPTSTLRRHKRHNSLPKNALYPRHTTLQESL **::*:* ** .***:: * ******************* ****:**** C1 DDDDD-EEEESAQQKD-QQTKSKICHSDTELDPPQKA-KQCHIAGQNHQS C2 DDDDDDEEEERAQQKD-QQTKSKICHSDTELDPPQKS-KQCHIAGQNHQS C3 DDDDDDEEEESPQQKE-KQAKPKGCHSDTELDPPQKA-KQCHIAGQNHQT C4 DDDDE-EEEESPQQKD-QQAKTKICHSDTELDPPQKA-KQCHIAGQNHQS C5 DDDDDDVDGGEEDLKE-QQT--KFCHSDTELDPPQKTGKQCHIGGQNHQS C6 DDDDDEDEEVSSRNKDQQDHKTKGCHSDTELDPPQKA-KQCHIAGQNHQT C7 DDDDDDEEEKD------QQGNTKFCHSDTELDPPQKP-KQCHIAGQNHQT C8 DDDDEEEEEEVRKE---QQSKTKFCHSDTELDPPQNQ-KQCHIAGQNHQS C9 DDDDD-EEDERARHKD-SPSKTKICHSDTELDPPQNA-KQCHANGQDHQT ****: : . * ***********: **** **:**: C1 DYLQLPSVCTCPYFGDRPLQNCVKSAEVKIISSAFRVTTTTT-AVSSSPS C2 DYLQLPSVCTCPYFGDRPLQNCVKSAEVKIISSAFRVTTTTT-AVSSSPS C3 DYLQLPSVCTCPYFGDRPLQNCVKSAEVKIISSAFRVTTTTT-AVSSSPS C4 DYLQLPSVCTCPYFGDRPLQNCVKSAEVKIISSAFRVTTTTT-AVSSSPS C5 DYLQLPSVCTCPYFGDRPLQNCVKTAEVKIISSAFRVTTTTTTAVSSSPS C6 DYLQLPSVCTCPYFGDRPLQNCVKTAEVKIVSSAFRVTTTTTTAVSSSPS C7 DYLQLPSVCTCPYFGDRPLQNCVKTAEVKIISSAFRVTTTTT-AVSSSPS C8 DYLQLPSVCTCPYFGDRPLQNCVKTAEVKIISSAFRVTTTTT-AVSSSPS C9 DYLQLPSVCTCPYFGDRPLQNCVKTAEVKIISSAFRVTTTTT-AVSSSPS ************************:*****:*********** ******* C1 EMELLMCSSG-NKKSLTSSVSAGITGG----PAGAAP--ATVGSTLSPHS C2 EMELLMCSSG-NKKSLTSSVSAGMTGG----PAGAAP--ATVGSTLSPHS C3 EMELLMCSGG-NKKSLTSSVSAGTTGG----PAGAAS--AAVGSTLSPHS C4 EMELLMCSSG-NKKSMTSSVSAGTTGG----PAGAGP--ATGGSTLSPNS C5 EMELLMCTGGGTKKSLTSSVSAGMTGG----PGGGGPPPATVGSTLSPHS C6 EMELLMCSGG-NKKSLTSSVSAGMTGGGS--AAGGAGPPATIGSTLSPHS C7 EMELLMCSGG-NKKSLTSSVSAGMTGG----SAGGGGPPPTGGSTLSPHS C8 EMELLMCSAG-NKKSLTSSVSAGITGG----SSGAGPP-QTGGSTLSPHS C9 EMELLMCSGG-KKKSLTSSVSAGMTGGSAGGGAGGGGPPATCGSTLSPHS *******:.* .***:******* *** .*.. : ******:* C1 AHNQGSSLTVQSDGSGYLAAPGTPCPGRRKLSISKTASVVTWDSSRHRRR C2 AHNQGSSLTVQSDGSGYLAAPGTPCPGRRKLSISKTASVVTWDSSRHRRR C3 AHNQGSSLTVQSDGSGYLAAPGTPCPGRRKLSISKTASVVTWDSSRHRRR C4 AHNQGSSLTVQSDGSGYLAAPGTPCPGRRKLSISKTASVVTWDSSRHRRR C5 AHNQGSSLTVQSDGSGYLAAPGTPCPGRRKLSISKTASVVTWDSSRHRRR C6 VHNQGSSLTVQSDSSGYLAAPGTPCPGRRKLSISKTASVVTWDSSRHRRR C7 AHNQGSSLTVQSDGSGYLAAPGTPCPGRRKLSISKTASVVTWDSSRHRRR C8 AQNQGSSLTVQSDGSGFLAAPGTPCPGRRKLSISKTASVVTWDSGRHRRR C9 AHNQGSSLTVQSDGSGYLAAPGTPCPGRRKLSISKTASVVTWDSSRHRRR .:***********.**:***************************.***** C1 GSSFGGVRTSLLLTPTKTATTS-NSSTPLRRSATLRSHQNMNYQGAGECG C2 GSSFGGVRTSLLLTPTKTATTS-NSSTPLRRSATLRSHQNMNYQGAGECG C3 GSSFGGVRTSLLLTPTKTATAF-NSSTPLRRSATLRSHQNMNYQGAGDCG C4 GSSFGGVRTSLLLTPTKTATAF-NSSTPLRRSATLRSHQNMNYQGAGDCG C5 GSSFGGVRTSLLLTPTKTATASTASSTPLRRSATLRSHQNMNYQGQGDCG C6 GSSFGGVRTSLLLTPTKTATPT-TSSTPLRRSATLRSHQNMNYQGAGDCG C7 GSSFGGVRTSLLLTPTKTATPS-TSSTPLRRSATLRSHQNMNYQGAGDCG C8 GSSFGGVRTSLLLTPTKTATAS-TSSTPLRRSATLRSHQNMNYQGAGECG C9 GSSFGGVRTSLLLTPTKTATAS-TSSTPLRRSATLRSHQNMNYQGAGECG ********************. ********************* *:** C1 G-KTRTTTSSPCMLQRQQTVRSHHSRNSSVISRNSSRHGRIIRLEQKATK C2 G-KTRTTTSSPCMLQRQQTVRSHHSRNSSVISRNSSRHGRIIRLEQKATK C3 S-KTRTTTSSPCMLQRQQTVRSHHSRNSSVISRNSSRHGRIIRLEQKATK C4 A-KTRTTTSSPCMLQRQQTVRSHHSRNSSVISRNSSRHGRIIRLEQKATK C5 AGKTRTTTSSPCMLQRQQTVRSHHSRNSSVISRNSSRHGRIIRLEQKATK C6 G-KTRNTTSSPCMLQRQQTVRSHHSRNSSVISRNSSRHGRIIRLEQKATK C7 G-KTRTTTSSPCMLQRQQTVRSHHSRNSSVISRNSSRHGRIIRLEQKATK C8 G-KARTTTSSPCMLQRQQTVRSHHSRNSSVISRNSSRHGRIIRLEQKATK C9 G-KARTTTSSPCMLQRQQTVRSHHSRNSSVISRNSSRHGRIIRLEQKATK . *:*.******************************************** C1 VLGVVFFTFVILWSPFFVLNLLPTVCAECEERISHWVFDVVTWLGYASSM C2 VLGVVFFTFVILWSPFFVLNLLPTVCAECEERISHWVFDVVTWLGYASSM C3 VLGVVFFTFVILWSPFFVLNLLPTVCAECEERISHWVFDVVTWLGYASSM C4 VLGVVFFTFVILWSPFFVLNLLPTVCAECEERISHWVFDVVTWLGYASSM C5 VLGVVFFTFVILWSPFFVLNLLPTVCAECEERISHWVFDVVTWLGYASSM C6 VLGVVFFTFVILWSPFFVLNLLPTVCAECEERISHWVFDVVTWLGYASSM C7 VLGVVFFTFVILWSPFFVLNLLPTVCAECEERISHWVFDVVTWLGYASSM C8 VLGVVFFTFVILWSPFFVLNLLPTVCAECEERISHWVFDVVTWLGYASSM C9 VLGVVFFTFVILWSPFFVLNLLPTVCAECEERISHWVFDVVTWLGYASSM ************************************************** C1 VNPIFYTIFNKVFRQAFKKVLLCRYSSTSAWRPSRooooooooooooo-- C2 VNPIFYTIFNKVFRQAFKKVLLCRYSSTSAWRPSRoooooooooooo--- C3 VNPIFYTIFNKVFRQAFKKVLLCRYSSTSAWRPSRooooooo-------- C4 VNPIFYTIFNKVFRQAFKKVLLCRYSSTSAWRPSRooooooo-------- C5 VNPIFYTIFNKVFRQAFKKVLLCRYSSTSAWRPSRooooo---------- C6 VNPIFYTIFNKVFRQAFKKVLLCRYSSTSAWRPSRooooooo-------- C7 VNPIFYTIFNKVFRQAFKKVLLCRYSSTSAWRPSRooooooooooooooo C8 VNPIFYTIFNKVFRQAFKKVLLCRYSSTSAWRPSRoo------------- C9 VNPIFYTIFNKVFRQAFKKVLLCRYSNTSAWRPSR--------------- **************************.******** C1 -- C2 -- C3 -- C4 -- C5 -- C6 -- C7 oo C8 -- C9 -- PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:04 - Revision 1613 - Build 427) -full_log S [0] -genepred_score S [0] nsd -run_name S [0] -mem_mode S [0] mem -extend D [1] 1 -extend_mode S [0] very_fast_triplet -max_n_pair D [0] 10 -seq_name_for_quadruplet S [0] all -compact S [0] default -clean S [0] no -do_self FL [0] 0 -do_normalise D [0] 1000 -template_file S [0] -setenv S [0] 0 -template_mode S [0] -flip D [0] 0 -remove_template_file D [0] 0 -profile_template_file S [0] -in S [0] -seq S [0] -aln S [0] -method_limits S [0] -method S [0] -lib S [0] -profile S [0] -profile1 S [0] -profile2 S [0] -pdb S [0] -relax_lib D [0] 1 -filter_lib D [0] 0 -shrink_lib D [0] 0 -out_lib W_F [0] no -out_lib_mode S [0] primary -lib_only D [0] 0 -outseqweight W_F [0] no -dpa FL [0] 0 -seq_source S [0] ANY -cosmetic_penalty D [0] 0 -gapopen D [0] 0 -gapext D [0] 0 -fgapopen D [0] 0 -fgapext D [0] 0 -nomatch D [0] 0 -newtree W_F [0] default -tree W_F [0] NO -usetree R_F [0] -tree_mode S [0] nj -distance_matrix_mode S [0] ktup -distance_matrix_sim_mode S [0] idmat_sim1 -quicktree FL [0] 0 -outfile W_F [0] default -maximise FL [1] 1 -output S [1] score_ascii html score_ascii -len D [0] 0 -infile R_F [1] /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln -matrix S [0] default -tg_mode D [0] 1 -profile_mode S [0] cw_profile_profile -profile_comparison S [0] profile -dp_mode S [0] linked_pair_wise -ktuple D [0] 1 -ndiag D [0] 0 -diag_threshold D [0] 0 -diag_mode D [0] 0 -sim_matrix S [0] vasiliky -transform S [0] -extend_seq FL [0] 0 -outorder S [0] input -inorder S [0] aligned -seqnos S [0] off -case S [0] keep -cpu D [0] 0 -maxnseq D [0] 1000 -maxlen D [0] -1 -sample_dp D [0] 0 -weight S [0] default -seq_weight S [0] no -align FL [1] 1 -mocca FL [0] 0 -domain FL [0] 0 -start D [0] 0 -len D [0] 0 -scale D [0] 0 -mocca_interactive FL [0] 0 -method_evaluate_mode S [0] default -evaluate_mode S [1] t_coffee_fast -get_type FL [0] 0 -clean_aln D [0] 0 -clean_threshold D [1] 1 -clean_iteration D [1] 1 -clean_evaluate_mode S [0] t_coffee_fast -extend_matrix FL [0] 0 -prot_min_sim D [40] 40 -prot_max_sim D [90] 90 -prot_min_cov D [40] 40 -pdb_type S [0] d -pdb_min_sim D [35] 35 -pdb_max_sim D [100] 100 -pdb_min_cov D [50] 50 -pdb_blast_server W_F [0] EBI -blast W_F [0] -blast_server W_F [0] EBI -pdb_db W_F [0] pdb -protein_db W_F [0] uniprot -method_log W_F [0] no -struc_to_use S [0] -cache W_F [0] use -align_pdb_param_file W_F [0] no -align_pdb_hasch_mode W_F [0] hasch_ca_trace_bubble -external_aligner S [0] NO -msa_mode S [0] tree -master S [0] no -blast_nseq D [0] 0 -lalign_n_top D [0] 10 -iterate D [1] 0 -trim D [0] 0 -split D [0] 0 -trimfile S [0] default -split D [0] 0 -split_nseq_thres D [0] 0 -split_score_thres D [0] 0 -check_pdb_status D [0] 0 -clean_seq_name D [0] 0 -seq_to_keep S [0] -dpa_master_aln S [0] -dpa_maxnseq D [0] 0 -dpa_min_score1 D [0] -dpa_min_score2 D [0] -dpa_keep_tmpfile FL [0] 0 -dpa_debug D [0] 0 -multi_core S [0] templates_jobs_relax_msa_evaluate -n_core D [0] 0 -max_n_proc D [0] 0 -lib_list S [0] -prune_lib_mode S [0] 5 -tip S [0] none -rna_lib S [0] -no_warning D [0] 0 -run_local_script D [0] 0 -plugins S [0] default -proxy S [0] unset -email S [0] -clean_overaln D [0] 0 -overaln_param S [0] -overaln_mode S [0] -overaln_model S [0] -overaln_threshold D [0] 0 -overaln_target D [0] 0 -overaln_P1 D [0] 0 -overaln_P2 D [0] 0 -overaln_P3 D [0] 0 -overaln_P4 D [0] 0 -exon_boundaries S [0] -dump S [0] no -display D [0] 100 INPUT FILES Input File (S) /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 9 SEQUENCES [PROTEIN] Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length 917 type PROTEIN Struct Unchecked Multi Core Mode: 72 processors: gins S [0] default -proxy S [0] unset -email S [0] -clean_overaln D [0] 0 -overaln_param S [0] -overaln_mode S [0] -overaln_model S [0] -overaln_threshold D [0] 0 -overaln_target D [0] 0 -overaln_P1 D [0] 0 -overaln_P2 D [0] 0 -overaln_P3 D [0] 0 -overaln_P4 D [0] 0 -exon_boundaries S [0] -dump S [0] no -display D [0] 100 INPUT FILES Input File (S) /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 9 SEQUENCES [PROTEIN] Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length 917 type PROTEIN Struct Unchecked Multi Core Mode: 72 processors: --- Process Method/Library/Aln S/opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins S [0] default -proxy S [0] unset -email S [0] -clean_overaln D [0] 0 -overaln_param S [0] -overaln_mode S [0] -overaln_model S [0] -overaln_threshold D [0] 0 -overaln_target D [0] 0 -overaln_P1 D [0] 0 -overaln_P2 D [0] 0 -overaln_P3 D [0] 0 -overaln_P4 D [0] 0 -exon_boundaries S [0] -dump S [0] no -display D [0] 100 INPUT FILES Input File (S) /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 9 SEQUENCES [PROTEIN] Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length 917 type PROTEIN Struct Unchecked Multi Core Mode: 72 processors: --- Process Method/Library/Aln S/opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins S [0] default -proxy S [0] unset -email S [0] -clean_overaln D [0] 0 -overaln_param S [0] -overaln_mode S [0] -overaln_model S [0] -overaln_threshold D [0] 0 -overaln_target D [0] 0 -overaln_P1 D [0] 0 -overaln_P2 D [0] 0 -overaln_P3 D [0] 0 -overaln_P4 D [0] 0 -exon_boundaries S [0] -dump S [0] no -display D [0] 100 INPUT FILES Input File (S) /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 9 SEQUENCES [PROTEIN] Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length 917 type PROTEIN Struct Unchecked Multi Core Mode: 72 processors: --- Process Method/Library/Aln S/opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins S [0] default -proxy S [0] unset -email S [0] -clean_overaln D [0] 0 -overaln_param S [0] -overaln_mode S [0] -overaln_model S [0] -overaln_threshold D [0] 0 -overaln_target D [0] 0 -overaln_P1 D [0] 0 -overaln_P2 D [0] 0 -overaln_P3 D [0] 0 -overaln_P4 D [0] 0 -exon_boundaries S [0] -dump S [0] no -display D [0] 100 INPUT FILES Input File (S) /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 9 SEQUENCES [PROTEIN] Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length 917 type PROTEIN Struct Unchecked Multi Core Mode: 72 processors: --- Process Method/Library/Aln S/opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins S [0] default -proxy S [0] unset -email S [0] -clean_overaln D [0] 0 -overaln_param S [0] -overaln_mode S [0] -overaln_model S [0] -overaln_threshold D [0] 0 -overaln_target D [0] 0 -overaln_P1 D [0] 0 -overaln_P2 D [0] 0 -overaln_P3 D [0] 0 -overaln_P4 D [0] 0 -exon_boundaries S [0] -dump S [0] no -display D [0] 100 INPUT FILES Input File (S) /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 9 SEQUENCES [PROTEIN] Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length 917 type PROTEIN Struct Unchecked Input File /opt/ADOPS/1/5-HT2B-PD/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length 917 type PROTEIN Struct Unchecked Multi Core Mode: 72 processors: --- Process Method/Library/Aln S/opt/ADO