--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Dec 08 07:29:19 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/418/Tm1-PH/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/418/Tm1-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/418/Tm1-PH/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/418/Tm1-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -7121.64         -7136.96
2      -7121.78         -7134.62
--------------------------------------
TOTAL    -7121.71         -7136.36
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/418/Tm1-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/418/Tm1-PH/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/418/Tm1-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.728574    0.002022    0.641670    0.816059    0.726229   1443.04   1472.02    1.000
r(A<->C){all}   0.085663    0.000122    0.064915    0.107255    0.085002    989.84   1062.04    1.000
r(A<->G){all}   0.226912    0.000407    0.189438    0.267601    0.226046    902.17   1020.03    1.000
r(A<->T){all}   0.118092    0.000290    0.087216    0.152846    0.117613   1042.35   1084.83    1.000
r(C<->G){all}   0.102788    0.000143    0.078010    0.125138    0.102656    908.68    983.76    1.000
r(C<->T){all}   0.384142    0.000718    0.335028    0.438543    0.383756    719.75    886.38    1.000
r(G<->T){all}   0.082402    0.000239    0.053334    0.113294    0.081504    798.48   1011.72    1.000
pi(A){all}      0.312770    0.000088    0.293602    0.330164    0.312781   1257.95   1280.41    1.000
pi(C){all}      0.282736    0.000088    0.263246    0.299765    0.282516   1188.09   1192.97    1.000
pi(G){all}      0.251763    0.000074    0.234573    0.267594    0.251994   1032.33   1127.16    1.000
pi(T){all}      0.152730    0.000053    0.137557    0.166713    0.152774    951.96   1114.38    1.000
alpha{1,2}      0.232547    0.001589    0.160820    0.313748    0.229552   1014.21   1079.29    1.000
alpha{3}        1.859933    0.424948    0.787949    3.142075    1.746071    919.88   1055.58    1.000
pinvar{all}     0.334032    0.003810    0.213478    0.451512    0.340273    934.55    989.41    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	-6092.412671
Model 2: PositiveSelection	-6088.49043
Model 0: one-ratio	-6207.39269
Model 3: discrete	-6082.896597
Model 7: beta	-6089.63645
Model 8: beta&w>1	-6083.116789


Model 0 vs 1	229.96003799999926

Model 2 vs 1	7.844482000000426

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Tm1-PH)

            Pr(w>1)     post mean +- SE for w

    36 K      0.974*        5.342
    37 P      0.620         3.763
    38 K      0.896         4.991

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_Tm1-PH)

            Pr(w>1)     post mean +- SE for w

    35 V      0.529         1.368 +- 0.522
    36 K      0.887         1.747 +- 0.760
    37 P      0.843         1.706 +- 0.748
    38 K      0.858         1.725 +- 0.764
   133 R      0.646         1.501 +- 0.638
   143 Q      0.582         1.406 +- 0.520
   279 T      0.612         1.442 +- 0.555
   323 L      0.501         1.338 +- 0.494


Model 8 vs 7	13.039322000000539

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_Tm1-PH)

            Pr(w>1)     post mean +- SE for w

    36 K      0.993**       3.950
    37 P      0.920         3.716
    38 K      0.972*        3.882

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_Tm1-PH)

            Pr(w>1)     post mean +- SE for w

    32 A      0.692         1.222 +- 0.446
    35 V      0.800         1.329 +- 0.371
    36 K      0.987*        1.496 +- 0.108
    37 P      0.981*        1.492 +- 0.122
    38 K      0.982*        1.493 +- 0.119
    39 P      0.564         1.089 +- 0.496
    49 A      0.706         1.236 +- 0.437
   108 S      0.721         1.251 +- 0.429
   129 S      0.691         1.231 +- 0.427
   133 R      0.904         1.429 +- 0.251
   140 P      0.614         1.141 +- 0.482
   142 T      0.763         1.301 +- 0.383
   143 Q      0.885         1.414 +- 0.269
   154 C      0.516         0.997 +- 0.558
   279 T      0.900         1.427 +- 0.252
   322 A      0.684         1.214 +- 0.449
   323 L      0.765         1.295 +- 0.400
   324 I      0.632         1.161 +- 0.473
   327 D      0.513         1.004 +- 0.545
   329 A      0.693         1.223 +- 0.444
   333 G      0.762         1.300 +- 0.383
   375 Q      0.662         1.192 +- 0.460

>C1
MYEKTLNIGTAKVNNAYEWQKVRYNNKPQPTTTAAAAVKPKPQQQQVQKQ
KNATKAAPATTTAATTTATVPPLAGNSVTVKQGPKIKFVGNAARRQSLAH
QIKRAHRHLLTSGGQDKQPQQKQKTQVQPQSGKTVAKPKQRQQKQLFKSD
KAKEKSSRQQRKRAGTRSTRNPRTQSESSGLSSRWCSIEEQLNLLDDLLY
YCDEEAELYLAQLYERFETLRRSRSSSPVSDFWSDSDMEHDDSSTSGTGS
HTASNTSLVPASLKRRGHQHHPRFSGTRRPNVPNVQEILAALYRGDSKSA
LSNLRGETQPEEEQPQQQTEEVLPPSRSTLSLPLSESVTNSLGSNSPTPT
DESSVQDEGASNPAAALIAEDAAPPAGTTTSKSKKKKREKGERSEKSDKS
EKSDRKKKSSGKKERSKRSNPMEQSSDSLATDLSAGAIDEGIALADDDDN
QAAEWSKLRCTSEAAEIVAEREARRNKGRCADYPGLAFGRSIFSSDTMMK
FNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEEDLERSEERLGSATAK
LSEASQAADESERARKILENRALADEERMDALENQLKEARFLAEEADKKY
DEVQLKTNLSSIKLSNNNNNSNSNNIEISKSESCNASDIGGTNNNNASRT
IASAAVGEETSTLSSTSHEHNNNPNNDTooo
>C2
MYEKTLNIGTAKVNNAYEWQKVRYNNKPQPTTTTAAAVKPKPQQQAQKQK
NATKAAPATTTAATTTATVPPLAGNSVTVKQGPKIKFVGNAARRQSLAHQ
IKRAHRHLLTSGGQDKQPQQKQKTQVQPQSGKTVAKPKQRQQKQLFKSDK
AKEKFSRQQRKRGGTRSTRNPRTQSESSGLSSRWISIEEQLNLLDDLLYY
CDEEAELYLAQLYERFETLRRSRSSSPVSDFWSDSDMEHDDSSTSGTGSH
TASNTSLVPASLKRRGHQHHPRFSGTRRPNVPNVQEILAALYRGDSKSAL
SNLRGETQPEEEQPQQQPEEMLPPSRSTLSLPLSESVTNSLGSNSPTPTD
ESSVQDEGASNPAAASIAEDAAPPAATTTSKSKKKKREKCERSEKSDKTE
KSDRKKKSSSKKERSKRSNPMELSSDSLVTDLSAGAIDEGIALADDDDNQ
AAEWSKLRCTSEAAEIVAEREARRNKGRCADYPGLAFGRSIFSSDTMMKF
NIIRNELHNIMNTQLKRAESEVAALNRRIQLLEEDLERSEERLGSATAKL
SEASQAADESERARKILENRALADEERMDALENQLKEARFLAEEADKKYD
EVQLKTNLSSIKLSNNNNNSNSNNIEISKSESCNASDIGGTNNNNASRTI
ASAAVGEETSTLSSTSHEHNNNPNNDToooo
>C3
MYEKTLNIGTAKVNNAYEWQKVRYNNKPQPTTTTAAAVKPKPQQQQAQKQ
KNATKAAPATTTAATTTATVPPLAGNSVTVKQGPKIKFVGNAARRQSLAH
QIKRAHRHLLTSGGQDKQPQQKQKTQVQPQSGKTVAKPKQRQQKQLFKSD
KAKEKFSRQQRKRGGTRSTRNPRTQSESSGLSSRWISIEEQLNLLDDLLY
YCDEEAELYLAQLYERFETLRRSRSSSPVSDFWSDSDMEHDDSSTSGTGR
HTASNTSLVPASLKRRGHQHHPRFSGTRRPNVPNVQEILAALYRGDSKSA
LSNLRGETQPEEEQPQQQPEEMLPPSRSTLSLPLSESVTNSLGSNSPTPT
DESSVQDEGASNPAAASIAEDAAPPAATTTSKSKKKKREKGERSEKSEKS
EKSDRKKKSSSKKERSKRSNPMELSSDSLATDLSAGTIDEGIALADDDDN
QAAEWSKLRCTSEAAEIVAEREARRNKGRCADYPGLAFGRSIFSSDTMMK
FNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEEDLERSEERLGSATAK
LSEASQAADESERARKILENRALADEERMDALENQLKEARFLAEEADKKY
DEVQLKTNLSSIKLSNNNNNSNSNNIEISKSESCNASDIGGTNNNNASRT
IASAAVGEETSTLSSTSHEHNNNPNNDTooo
>C4
MYEKTLNIGTAKVNNAYEWQKVRYNNKPQTSTTTTAAVKAKQQQQTQRLK
NATKAAAATTTAATTTATTATVPPLAGNSITVKQGPKIKFVGNAARRQSL
AHQIKRAHRHLLTSGGQDKQPQQKQKTQVQPQSGKTVAKPKQRQQKQLFK
SDKAKEKCSRQQRKRAGTRSTRNPRTQSESSGLSSRWCSIEEQLNLLDDL
LYYCDEEAELYLAQLYERFETLRRSRSSTPVSDFWSDSDMEHDDSSTSGT
GSHTASNTSLVPASLKRRGHQHHPRFSGTRRPNVPNVQEILAALYRGDSK
SALSNLRGETQPPPEEEQTQPEQVLPPSRSTLSLPLSESVTNSLGSNSPT
PTDESSVQDEGASHPAAASIAGDAAPPAATATSKSKKKKREKGEKSEKSE
KSEKSDRKKKSSGKKERSKRSNAMEVSSDSLATDLSAGAIDEGIALADDD
DNQAAEWSKLRCTSEAAEIVAEREARRNKGRCADYPGLAFGRSIFSSDTM
MKFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEEDLERSEERLGSAT
AKLSEASQAADESERARKILENRALADEERMDALENQLKEARFLAEEADK
KYDEVQLKTNLSSIKLSNNNNNNNSNSNNIEISNASDIGGTNNNNASRTI
ASAAVGEETSTLSSTSHEHNNNPNNDToooo
>C5
MYEKTLNIGTAKVNNAYVWQKVSYNNKPHPTTTTTAPAVKVKQKNATKAA
PATTTAATTTARAAATVPPLTGNSITVKQGPKIKFVGNATRRQSLAHQIK
RAHRHLLTSGGQDKQPQQKQKTQVQPLSGKTVAKPKQRQQKQLFKSDKAK
EKCSRQQRKRAGTRSTRNPRAQSESSGLSSRWCSIEEQLNLLDDLLYYCD
EEAELYLAQLYERFETLRRSRSSTPVSDFWSDSEMEHDDSSTSGTGSHTA
SNTSLVPASLKRRGHQHHPRFSGTRRPNVPNVQEILAALYRGDSKSALSN
LRGETQPPPEEEQPQQQPEEVLPPSRSTLSLPLSESVTNSLGSNSPTPTD
ESSVQDEGATHPAASSIAEDAAPPAATTTSKSKKKKREKGEKSEKSEKSD
RKKKSSGKKERSKRSNPMEVSSDSLATDLSAGAIDEGIALADDDDNQAAE
WSKLRCTSEAAEIVAEREARRNKGRCADYPGLAFGRSIFSSDTMMKFNII
RNELHNIMNTQLKRAESEVAALNRRIQLLEEDLERSEERLGSATAKLSEA
SQAADESERARKILENRALADEERMDALENQLKEARFLAEEADKKYDEVQ
LKTNLSSIKLSNNNNNSNSNNIEISKPEPCNASDIGGTNNNNASRTIASA
AVGEETSTLSSTSHEHNNNPNNDTooooooo
>C6
MYEKTLNIGTAKVNNAYEWQKVRYNNKPQPTTTAVKVKQQPQPIQKQKNA
TTKVAPTTTTAPPLTGNSITVKQGPKIKFVGNAARRQSLAHQIKRAHRHL
LTSGGQDKQPQQKQKTQVQPSGKTVAKPKQRSKQLLKGDKKPKQQQPRKT
RRKTRADSQSSGLSSRWCSIEEQLNLLDDLLYYCDEEAELYLAQLYERFD
SLRRSRSNSCSSSPASDFWSDESDMEHHDDSSTSGTGSHSSLVPASLKRR
GHQHHPRFSGTRRPNVPNVQEILAALYRGDSKSALSNLRGETQPAAAPEE
EAPVLPPSRSTLSLPLSESVTNSLGSNSPTPTDESSVQDEVATVSVAEGA
APPAVTTTTSSAKSKKKKREKSEKSEKSEKSEKKKKSSGKKERSKRSNPM
EMSSDSLATDISGGAIDEGIALADDDDNQAAEWSKLRCTSEAAEIVAERE
ARRNKGRCADYPGLAFGRSIFSSDTMMKFNIIRNELHNIMNTQLKRAESE
VAALNRRIQLLEEDLERSEERLGSATAKLSEASQAADESERARKILENRA
LADEERMDALENQLKEARFLAEEADKKYDEVQLKTNLSSIKLSNNNNNSN
SNNININISKSELCNASDIGGTNNNNASRTIASAAVGEETSTLSSTSHEH
NNNPNNDTooooooooooooooooooooooo
>C7
MYEKTLNIGTAKVNNAYEWQKVRYNNKPQPTTTTATAVKVKQQQLQKQKN
ATKAAPATTTTTAPPLTGNSITVKQGPKIKFVGNAARRQSLAHQIKRAHR
HLLTSGGQDKQPQQKQKTQVPQTSGKTVAKAKPRQKQLLKSDKAKEKPKQ
QRKRAVTRNTRNPRGQSESSGLSSRWCSIEEQLNLLDDLLYYCDEEAELY
LAQLYERFKTLRRSRSSSVASDFWSDSDMEHDDSSTSGTGSHTASNNSLV
PSSLKRRGHQHHPRFSGTRRPNVPNVQEILAALYRGDSKSALSNLRGETQ
PEEEQPQQQQQSEEVLHPSRSTLSLPLSESVTNSLGSNSPTPTDESSVQD
EGASNPAATSIAEGAIPPAPITTSKSKKKKREKGEKLEKSEKSEKSDRKK
KSSGKKERSKRSNPMELSSDSLATDISAGAIDEGIALADDDDNQAAEWSK
LRCTSEAAEIVAEREARRNKGRCADYPGLAFGRSIFSSDTMMKFNIIRNE
LHNIMNTQLKRAESEVAALNRRIQLLEEDLERSEERLGSATAKLSEASQA
ADESERARKILENRALADEERMDALENQLKEARFLAEEADKKYDEVQLKT
NLSSIKLSNNNNNSNSNNINISKSELCNANAIGGTNNNNASRTIASAAVG
EETSTLSSTSHEHNNNPNNDToooooooooo
>C8
MYEKTLNIGTAKVNNAYAWQKVRYNNKPQATTTTTTASVKVKQQQPQKQK
NATKAAPTTTTTSTTKPTVLPLTGNSITVKQGPKIKFVGNAARRQSLAHQ
IKRAHRHLLTSGGQDKQPQQKQKAQVLPQTGKTVAKPKPKQKHLLKSDKT
REKQKQQQKKRGVAARNTCKRRAASESSGLSSRWCSIEEQLNLLDDLLYY
CDEEAELYLAQLYERFETLQRSSSQSSSPASDFWSDSDMEHDDSSTSGTG
SQTASNISLVPASLKRRGHQHHPRFSGTRRPNVPNVQEILAALYRGDSKS
ALSNLRGETQPEEEQPQQQEEGLPPSRSTLSLPLSESVTNSLGSNSPTPT
DESSVQDEGASNPATAPKGEESAPPAATTSTSKTKKKKREKGEKSEKSDK
SEKSDRKKKSSGKKERSKRSNAMELSSDSLATDISAGAIDEGIALADDDD
NQSAEWSKLRCTSEAAEIVAEREARRNKGRCADYPGLAFGRSIFSSDTMM
KFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEEDLERSEERLGSATA
KLSEASQAADESERARKILENRALADEERMDALENQLKEARFLAEEADKK
YDEVQLKTNLSSIKLSNNNNNSNSNNTNMNISKPELCNDSAIGGTNNNNA
SRTIASAAVGEETSTLSSTSHEHNNNPNNDT
>C9
MYEKTLNIGTAKVNNAYEWQKVRYNNKPQTTTTTPALKVKQQQPQRQKNA
TKAVPTTTATLPPLTGNSVTVIQGPKIKFVGYAARRQSLAHQIKRAHRHL
LTSGGQDKQPQHKQKAQVLPQTGKTVAKPKQKQKQLLKSDKSRGRHKQQQ
HQRKQGAGRNTRNPRAPSESSGLSSRWCSIEEQLNLLDDLLYYCDEEAEL
YLAQLYERFETLQRNSRGSSPASDFWSDSDMEHDDSSTSGTGSHTASNTS
LVPASLKRRGHQHHPRFSGTRRPNVPNVQEILAALYRGDSKSALSNLRGE
IQPEEEQQPPEEVVPPSRSTLSLPLSESVTNSLGSNSPTPTDESSVQDEG
ASNPPTAPTGEGAVPPAVTTTSKSKKKKREKGEKSDKSEKSDRKKKSSGK
KERSKRSNPMELSSDSLATDLSAGAIDEGIALADDDDNQAAEWSKLRCTS
EAAEIVAEREARRNKGRCADYPGLAFGRSIFSSDTMMKFNIIRNELHNIM
NTQLKRAESEVAALNRRIQLLEEDLERSEERLGSATAKLSEASQAADESE
RARKILENRALADEERMDALENQLKEARFLAEEADKKYDEVQLKTNLSST
KLSNNNNNSNSNNININISKSELCNASAIGGTNNNNASRTIASAAVGEET
STLSSTSHEHNNNPNNDTooooooooooooo
>C10
MYEKTLNIGTAKVNNAYEWQTVRYNNKPQTTTITAAVKVKKQQPQKQKNA
TKAAPATTVLPLTGNSITVQQGPKIKFVGNAARRQSLAHQIKRAHRHLLT
SQDKPPQQKQKTQVLLQTGKTVAKPKQKQKQLLKSDKAREKQKQHHHQRK
SAANRNTRNRRPQSESSGLSSRWCSIEEQLNLLDDLLYYCDEEAELYLAQ
LYERFETLQGSSRGSSPASDFWSDSDMDHDDSSTSGTGSHTASNASLVPA
SLKRRGHQHHPRFSGTRRPNVPNVQEILAALYRGDSKSALSNLRGETQPD
EEQQQPEEVLPPSRNTLSLPLSESVTNSLGSNSPTPTDESSVQDEVASNP
PAASTGEGAVPPAVTTTSKSKKKKREKGEKSEKSEKSEKSDRKKKSSGKK
ERSKRSNPMELSSDSLATDLSAGAIDEGIALADDDDNQAAEWSKLRCTSE
AAEIVAEREASRNKRRCADYPGLAFGKSIFSSDTMMKFNIIRNELHNIMN
TQLKRAESEVAALNRRIQLLEEDLERSEERLGSATAKLSEASQAADESER
ARKILENRALADEERMDALENQLKEARFLAEEADKKYDEVQLKTNLSSTK
LSNNNNNSNSNNININISKSELCNASAIGGTNNNNASRTIASAAVGEETS
TLSSTSHEHNNNPNNDToooooooooooooo
CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=100, Nseq=10, Len=718 

C1              MYEKTLNIGTAKVNNAYEWQKVRYNNKPQPTTTAAAAVKPKPQQQQVQKQ
C2              MYEKTLNIGTAKVNNAYEWQKVRYNNKPQPTTTTAAAVKPKPQQQ-AQKQ
C3              MYEKTLNIGTAKVNNAYEWQKVRYNNKPQPTTTTAAAVKPKPQQQQAQKQ
C4              MYEKTLNIGTAKVNNAYEWQKVRYNNKPQ-TSTTTTAAVKAKQQQQTQRL
C5              MYEKTLNIGTAKVNNAYVWQKVSYNNKPHPTTTTTAPAVKVKQ-------
C6              MYEKTLNIGTAKVNNAYEWQKVRYNNKPQ---PTTTAVKVKQQPQPIQKQ
C7              MYEKTLNIGTAKVNNAYEWQKVRYNNKPQPTTTTATAVKVKQQQ--LQKQ
C8              MYEKTLNIGTAKVNNAYAWQKVRYNNKPQATTTTTTASVKVKQQQ-PQKQ
C9              MYEKTLNIGTAKVNNAYEWQKVRYNNKPQ--TTTTTPALKVKQQQ-PQRQ
C10             MYEKTLNIGTAKVNNAYEWQTVRYNNKPQ--TTTITAAVKVKKQQ-PQKQ
                ***************** **.* *****:   .: :.     :       

C1              KNATKAAPATTTAATTTA----TVPPLAGNSVTVKQGPKIKFVGNAARRQ
C2              KNATKAAPATTTAATTTA----TVPPLAGNSVTVKQGPKIKFVGNAARRQ
C3              KNATKAAPATTTAATTTA----TVPPLAGNSVTVKQGPKIKFVGNAARRQ
C4              KNATKAAAATTTAATTTA-TTATVPPLAGNSITVKQGPKIKFVGNAARRQ
C5              KNATKAAPATTTAATTTARAAATVPPLTGNSITVKQGPKIKFVGNATRRQ
C6              KNATTKVAPTTT----------TAPPLTGNSITVKQGPKIKFVGNAARRQ
C7              KNATKAAPATT---TTTA------PPLTGNSITVKQGPKIKFVGNAARRQ
C8              KNATKAAPTTTTTSTTKP----TVLPLTGNSITVKQGPKIKFVGNAARRQ
C9              KNATKAVPTTTA----------TLPPLTGNSVTVIQGPKIKFVGYAARRQ
C10             KNATKAAPAT------------TVLPLTGNSITVQQGPKIKFVGNAARRQ
                ****. ...*               **:***:** ********* *:***

C1              SLAHQIKRAHRHLLTSGGQDKQPQQKQKTQVQPQSGKTVAKPKQRQQKQL
C2              SLAHQIKRAHRHLLTSGGQDKQPQQKQKTQVQPQSGKTVAKPKQRQQKQL
C3              SLAHQIKRAHRHLLTSGGQDKQPQQKQKTQVQPQSGKTVAKPKQRQQKQL
C4              SLAHQIKRAHRHLLTSGGQDKQPQQKQKTQVQPQSGKTVAKPKQRQQKQL
C5              SLAHQIKRAHRHLLTSGGQDKQPQQKQKTQVQPLSGKTVAKPKQRQQKQL
C6              SLAHQIKRAHRHLLTSGGQDKQPQQKQKTQVQP-SGKTVAKPKQRS-KQL
C7              SLAHQIKRAHRHLLTSGGQDKQPQQKQKTQVPQTSGKTVAKAKPRQ-KQL
C8              SLAHQIKRAHRHLLTSGGQDKQPQQKQKAQVLPQTGKTVAKPKPKQ-KHL
C9              SLAHQIKRAHRHLLTSGGQDKQPQHKQKAQVLPQTGKTVAKPKQKQ-KQL
C10             SLAHQIKRAHRHLLTS--QDKPPQQKQKTQVLLQTGKTVAKPKQKQ-KQL
                ****************  *** **:***:**   :******.* :. *:*

C1              FKSDKAKEKSSRQQRKR--AGTRSTRNPRTQSESSGLSSRWCSIEEQLNL
C2              FKSDKAKEKFSRQQRKR--GGTRSTRNPRTQSESSGLSSRWISIEEQLNL
C3              FKSDKAKEKFSRQQRKR--GGTRSTRNPRTQSESSGLSSRWISIEEQLNL
C4              FKSDKAKEKCSRQQRKR--AGTRSTRNPRTQSESSGLSSRWCSIEEQLNL
C5              FKSDKAKEKCSRQQRKR--AGTRSTRNPRAQSESSGLSSRWCSIEEQLNL
C6              LKGDK---KPKQQQPRK------TRRKTRADSQSSGLSSRWCSIEEQLNL
C7              LKSDKAKEK-PKQQRKR--AVTRNTRNPRGQSESSGLSSRWCSIEEQLNL
C8              LKSDKTREKQKQQQKKR-GVAARNTCKRRAASESSGLSSRWCSIEEQLNL
C9              LKSDKSRGRHKQQQHQRKQGAGRNTRNPRAPSESSGLSSRWCSIEEQLNL
C10             LKSDKAREKQKQHHHQRKSAANRNTRNRRPQSESSGLSSRWCSIEEQLNL
                :*.**   :  ::: ::      .  : *  *:******** ********

C1              LDDLLYYCDEEAELYLAQLYERFETLRRSR----SSSPVSDFWSD-SDME
C2              LDDLLYYCDEEAELYLAQLYERFETLRRSR----SSSPVSDFWSD-SDME
C3              LDDLLYYCDEEAELYLAQLYERFETLRRSR----SSSPVSDFWSD-SDME
C4              LDDLLYYCDEEAELYLAQLYERFETLRRSR----SSTPVSDFWSD-SDME
C5              LDDLLYYCDEEAELYLAQLYERFETLRRSR----SSTPVSDFWSD-SEME
C6              LDDLLYYCDEEAELYLAQLYERFDSLRRSRSNSCSSSPASDFWSDESDME
C7              LDDLLYYCDEEAELYLAQLYERFKTLRRSR----SSSVASDFWSD-SDME
C8              LDDLLYYCDEEAELYLAQLYERFETLQRSSS--QSSSPASDFWSD-SDME
C9              LDDLLYYCDEEAELYLAQLYERFETLQRNS---RGSSPASDFWSD-SDME
C10             LDDLLYYCDEEAELYLAQLYERFETLQGSS---RGSSPASDFWSD-SDMD
                ***********************.:*: .     .*: .****** *:*:

C1              H-DDSSTSGTGSHTASNTSLVPASLKRRGHQHHPRFSGTRRPNVPNVQEI
C2              H-DDSSTSGTGSHTASNTSLVPASLKRRGHQHHPRFSGTRRPNVPNVQEI
C3              H-DDSSTSGTGRHTASNTSLVPASLKRRGHQHHPRFSGTRRPNVPNVQEI
C4              H-DDSSTSGTGSHTASNTSLVPASLKRRGHQHHPRFSGTRRPNVPNVQEI
C5              H-DDSSTSGTGSHTASNTSLVPASLKRRGHQHHPRFSGTRRPNVPNVQEI
C6              HHDDSSTSGTGSHSS----LVPASLKRRGHQHHPRFSGTRRPNVPNVQEI
C7              H-DDSSTSGTGSHTASNNSLVPSSLKRRGHQHHPRFSGTRRPNVPNVQEI
C8              H-DDSSTSGTGSQTASNISLVPASLKRRGHQHHPRFSGTRRPNVPNVQEI
C9              H-DDSSTSGTGSHTASNTSLVPASLKRRGHQHHPRFSGTRRPNVPNVQEI
C10             H-DDSSTSGTGSHTASNASLVPASLKRRGHQHHPRFSGTRRPNVPNVQEI
                * ********* :::    ***:***************************

C1              LAALYRGDSKSALSNLRGETQP--EEEQPQQQTEEVLPPSRSTLSLPLSE
C2              LAALYRGDSKSALSNLRGETQP--EEEQPQQQPEEMLPPSRSTLSLPLSE
C3              LAALYRGDSKSALSNLRGETQP--EEEQPQQQPEEMLPPSRSTLSLPLSE
C4              LAALYRGDSKSALSNLRGETQPPPEEEQ--TQPEQVLPPSRSTLSLPLSE
C5              LAALYRGDSKSALSNLRGETQPPPEEEQPQQQPEEVLPPSRSTLSLPLSE
C6              LAALYRGDSKSALSNLRGETQP----AAAPEEEAPVLPPSRSTLSLPLSE
C7              LAALYRGDSKSALSNLRGETQPEEEQPQQQQQSEEVLHPSRSTLSLPLSE
C8              LAALYRGDSKSALSNLRGETQP--EEEQP-QQQEEGLPPSRSTLSLPLSE
C9              LAALYRGDSKSALSNLRGEIQP--EEEQ--QPPEEVVPPSRSTLSLPLSE
C10             LAALYRGDSKSALSNLRGETQP--DEEQ--QQPEEVLPPSRNTLSLPLSE
                ******************* **              : ***.********

C1              SVTNSLGSNSPTPTDESSVQDEGASNPAAALIAEDAAPPAGTT-TSKSKK
C2              SVTNSLGSNSPTPTDESSVQDEGASNPAAASIAEDAAPPAATT-TSKSKK
C3              SVTNSLGSNSPTPTDESSVQDEGASNPAAASIAEDAAPPAATT-TSKSKK
C4              SVTNSLGSNSPTPTDESSVQDEGASHPAAASIAGDAAPPAATA-TSKSKK
C5              SVTNSLGSNSPTPTDESSVQDEGATHPAASSIAEDAAPPAATT-TSKSKK
C6              SVTNSLGSNSPTPTDESSVQDEVAT----VSVAEGAAPPAVTT-TTSSAK
C7              SVTNSLGSNSPTPTDESSVQDEGASNPAATSIAEGAIPPAPIT-TSKSKK
C8              SVTNSLGSNSPTPTDESSVQDEGASNPATAPKGEESAPPAATTSTSKTKK
C9              SVTNSLGSNSPTPTDESSVQDEGASNPPTAPTGEGAVPPAVTT-TSKSKK
C10             SVTNSLGSNSPTPTDESSVQDEVASNPPAASTGEGAVPPAVTT-TSKSKK
                ********************** *:       .  : ***  : *:.: *

C1              KKREKGERSEKSDKSEKSDRKKKSSGKKERSKRSNPMEQSSDSLATDLSA
C2              KKREKCERSEKSDKTEKSDRKKKSSSKKERSKRSNPMELSSDSLVTDLSA
C3              KKREKGERSEKSEKSEKSDRKKKSSSKKERSKRSNPMELSSDSLATDLSA
C4              KKREKGEKSEKSEKSEKSDRKKKSSGKKERSKRSNAMEVSSDSLATDLSA
C5              KKREKGEKSEKSE---KSDRKKKSSGKKERSKRSNPMEVSSDSLATDLSA
C6              SKKKKREKSEKSEKSEKSEKKKKSSGKKERSKRSNPMEMSSDSLATDISG
C7              KKREKGEKLEKSEKSEKSDRKKKSSGKKERSKRSNPMELSSDSLATDISA
C8              KKREKGEKSEKSDKSEKSDRKKKSSGKKERSKRSNAMELSSDSLATDISA
C9              KKREKGEKSDKSEKS---DRKKKSSGKKERSKRSNPMELSSDSLATDLSA
C10             KKREKGEKSEKSEKSEKSDRKKKSSGKKERSKRSNPMELSSDSLATDLSA
                .*::* *: :**:     ::*****.*********.** *****.**:*.

C1              GAIDEGIALADDDDNQAAEWSKLRCTSEAAEIVAEREARRNKGRCADYPG
C2              GAIDEGIALADDDDNQAAEWSKLRCTSEAAEIVAEREARRNKGRCADYPG
C3              GTIDEGIALADDDDNQAAEWSKLRCTSEAAEIVAEREARRNKGRCADYPG
C4              GAIDEGIALADDDDNQAAEWSKLRCTSEAAEIVAEREARRNKGRCADYPG
C5              GAIDEGIALADDDDNQAAEWSKLRCTSEAAEIVAEREARRNKGRCADYPG
C6              GAIDEGIALADDDDNQAAEWSKLRCTSEAAEIVAEREARRNKGRCADYPG
C7              GAIDEGIALADDDDNQAAEWSKLRCTSEAAEIVAEREARRNKGRCADYPG
C8              GAIDEGIALADDDDNQSAEWSKLRCTSEAAEIVAEREARRNKGRCADYPG
C9              GAIDEGIALADDDDNQAAEWSKLRCTSEAAEIVAEREARRNKGRCADYPG
C10             GAIDEGIALADDDDNQAAEWSKLRCTSEAAEIVAEREASRNKRRCADYPG
                *:**************:********************* *** *******

C1              LAFGRSIFSSDTMMKFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEE
C2              LAFGRSIFSSDTMMKFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEE
C3              LAFGRSIFSSDTMMKFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEE
C4              LAFGRSIFSSDTMMKFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEE
C5              LAFGRSIFSSDTMMKFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEE
C6              LAFGRSIFSSDTMMKFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEE
C7              LAFGRSIFSSDTMMKFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEE
C8              LAFGRSIFSSDTMMKFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEE
C9              LAFGRSIFSSDTMMKFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEE
C10             LAFGKSIFSSDTMMKFNIIRNELHNIMNTQLKRAESEVAALNRRIQLLEE
                ****:*********************************************

C1              DLERSEERLGSATAKLSEASQAADESERARKILENRALADEERMDALENQ
C2              DLERSEERLGSATAKLSEASQAADESERARKILENRALADEERMDALENQ
C3              DLERSEERLGSATAKLSEASQAADESERARKILENRALADEERMDALENQ
C4              DLERSEERLGSATAKLSEASQAADESERARKILENRALADEERMDALENQ
C5              DLERSEERLGSATAKLSEASQAADESERARKILENRALADEERMDALENQ
C6              DLERSEERLGSATAKLSEASQAADESERARKILENRALADEERMDALENQ
C7              DLERSEERLGSATAKLSEASQAADESERARKILENRALADEERMDALENQ
C8              DLERSEERLGSATAKLSEASQAADESERARKILENRALADEERMDALENQ
C9              DLERSEERLGSATAKLSEASQAADESERARKILENRALADEERMDALENQ
C10             DLERSEERLGSATAKLSEASQAADESERARKILENRALADEERMDALENQ
                **************************************************

C1              LKEARFLAEEADKKYDEVQLKTNLSSIKLSNNNNN--SNSNNIEISKSES
C2              LKEARFLAEEADKKYDEVQLKTNLSSIKLSNNNNN--SNSNNIEISKSES
C3              LKEARFLAEEADKKYDEVQLKTNLSSIKLSNNNNN--SNSNNIEISKSES
C4              LKEARFLAEEADKKYDEVQLKTNLSSIKLSNNNNNNNSNSNNIEIS----
C5              LKEARFLAEEADKKYDEVQLKTNLSSIKLSNNNNN--SNSNNIEISKPEP
C6              LKEARFLAEEADKKYDEVQLKTNLSSIKLSNNNNNSNSNNININISKSEL
C7              LKEARFLAEEADKKYDEVQLKTNLSSIKLSNNNNN--SNSNNINISKSEL
C8              LKEARFLAEEADKKYDEVQLKTNLSSIKLSNNNNNSNSNNTNMNISKPEL
C9              LKEARFLAEEADKKYDEVQLKTNLSSTKLSNNNNNSNSNNININISKSEL
C10             LKEARFLAEEADKKYDEVQLKTNLSSTKLSNNNNNSNSNNININISKSEL
                ************************** ********  **. *::**    

C1              CNASDIGGTNNNNASRTIASAAVGEETSTLSSTSHEHNNNPNNDTooo--
C2              CNASDIGGTNNNNASRTIASAAVGEETSTLSSTSHEHNNNPNNDToooo-
C3              CNASDIGGTNNNNASRTIASAAVGEETSTLSSTSHEHNNNPNNDTooo--
C4              -NASDIGGTNNNNASRTIASAAVGEETSTLSSTSHEHNNNPNNDToooo-
C5              CNASDIGGTNNNNASRTIASAAVGEETSTLSSTSHEHNNNPNNDTooooo
C6              CNASDIGGTNNNNASRTIASAAVGEETSTLSSTSHEHNNNPNNDTooooo
C7              CNANAIGGTNNNNASRTIASAAVGEETSTLSSTSHEHNNNPNNDTooooo
C8              CNDSAIGGTNNNNASRTIASAAVGEETSTLSSTSHEHNNNPNNDT-----
C9              CNASAIGGTNNNNASRTIASAAVGEETSTLSSTSHEHNNNPNNDTooooo
C10             CNASAIGGTNNNNASRTIASAAVGEETSTLSSTSHEHNNNPNNDTooooo
                 * . ****************************************     

C1              ------------------
C2              ------------------
C3              ------------------
C4              ------------------
C5              oo----------------
C6              oooooooooooooooooo
C7              ooooo-------------
C8              ------------------
C9              oooooooo----------
C10             ooooooooo---------
                                  




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/418/Tm1-PH/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/418/Tm1-PH/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: 10 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  681 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:
ins       	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/418/Tm1-PH/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: 10 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  681 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/418/Tm1-PH/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: 10 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  681 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/418/Tm1-PH/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: 10 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  681 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  681 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/418/Tm1-PH/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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