--- 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 