--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Dec 11 17:06:49 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
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=
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/pet1/Phyb_S22_15/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Phyb_S22_15/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/ADOPS1/pet1/Phyb_S22_15/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -12700.09        -12721.31
2     -12699.86        -12719.23
--------------------------------------
TOTAL   -12699.97        -12720.73
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/pet1/Phyb_S22_15/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Phyb_S22_15/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/ADOPS1/pet1/Phyb_S22_15/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         3.268125    0.011294    3.073699    3.488364    3.264066   1152.13   1256.43    1.000
r(A<->C){all}   0.135263    0.000106    0.114280    0.154271    0.134951    778.98    890.79    1.000
r(A<->G){all}   0.300452    0.000227    0.272027    0.329226    0.300194    641.03    717.47    1.000
r(A<->T){all}   0.098565    0.000048    0.084938    0.111547    0.098402    780.16    790.92    1.000
r(C<->G){all}   0.127302    0.000128    0.105594    0.150362    0.127127    817.46    887.87    1.000
r(C<->T){all}   0.258425    0.000189    0.231513    0.285170    0.258314    536.75    665.11    1.000
r(G<->T){all}   0.079992    0.000053    0.066148    0.094381    0.079734    938.58    972.83    1.000
pi(A){all}      0.303832    0.000092    0.285137    0.321933    0.303898    714.44    783.82    1.000
pi(C){all}      0.171523    0.000053    0.157414    0.186291    0.171538    655.93    761.76    1.000
pi(G){all}      0.194090    0.000067    0.179155    0.210579    0.193894    810.16    825.25    1.000
pi(T){all}      0.330555    0.000105    0.311400    0.350040    0.330190    864.51    895.15    1.000
alpha{1,2}      1.334385    0.033045    1.003783    1.675686    1.313239    828.32    946.01    1.000
alpha{3}        4.749783    0.945954    2.986935    6.686847    4.632338   1501.00   1501.00    1.000
pinvar{all}     0.046755    0.000451    0.003381    0.084092    0.046452   1006.59   1091.97    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	-11405.15486
Model 2: PositiveSelection	-11403.184732
Model 0: one-ratio	-11576.458564
Model 3: discrete	-11363.780608
Model 7: beta	-11378.955156
Model 8: beta&w>1	-11365.264844


Model 0 vs 1	342.60740799999985

Model 2 vs 1	3.940256000001682

Model 8 vs 7	27.380624000001262

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 1_Phybrida_S22_SLF10_AB933064)

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

    48 T      0.552         1.115
    51 F      0.934         1.423
    65 Y      0.953*        1.437
    67 F      0.977*        1.455
    83 K      0.673         1.220
    98 A      0.911         1.406
   101 I      0.832         1.346
   118 S      0.961*        1.443
   119 L      0.951*        1.436
   148 S      0.677         1.220
   150 S      0.759         1.288
   160 A      0.793         1.315
   176 C      0.587         1.154
   177 D      0.682         1.224
   180 M      0.708         1.246
   200 F      0.914         1.407
   203 W      0.807         1.325
   204 F      0.716         1.249
   219 F      0.717         1.258
   220 A      0.982*        1.459
   265 M      0.902         1.399
   266 P      0.913         1.407
   267 S      0.885         1.386
   270 T      0.710         1.249
   273 L      0.577         1.138
   318 H      0.584         1.150
   339 E      0.904         1.401
   352 A      0.707         1.244

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: 1_Phybrida_S22_SLF10_AB933064)

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

    51 F      0.816         1.383 +- 0.292
    65 Y      0.864         1.417 +- 0.262
    67 F      0.922         1.459 +- 0.210
    98 A      0.760         1.343 +- 0.315
   101 I      0.624         1.241 +- 0.361
   118 S      0.880         1.429 +- 0.248
   119 L      0.854         1.411 +- 0.266
   150 S      0.529         1.162 +- 0.380
   160 A      0.571         1.197 +- 0.373
   200 F      0.778         1.355 +- 0.315
   203 W      0.593         1.212 +- 0.370
   220 A      0.931         1.466 +- 0.198
   265 M      0.745         1.330 +- 0.323
   266 P      0.774         1.352 +- 0.315
   267 S      0.714         1.307 +- 0.335
   339 E      0.741         1.329 +- 0.320

>C1
MKELPQDVVIYIFVMLPVKSLLRFKCTDKTFCHIIKSSTFINLHLNHTTN
FNDELVLLKRSFETDEYNFYKSILSFLFAKEDYDFKPISPDVEIPHLTTT
AACICHRLIGPCNGLIVLTDSLTTIVFNPATLKYRLIPPCPFGIPRGFRR
SISGIGFGFDSDANDYKVVRLSEVYKEPCDKEMKVDIYDFSVDSWRELLG
QDVPFVFWFPCAEILYKRNFHWFAFADVVVILCFEMNTEKFHNMGMPDAC
HFADGKCYGLVILFKCMTLICYPDPMPSSPTEKLTDIWIMKEYGEKESWI
KRCSIRLLPESPLAVWKDEILLLHSKTGHLIAYDFNSNEVQELDLHGYPE
SLRIIIYRESLTAIPRNNDCIELQNFRCNooooooooooooooooo
>C2
MVDGIMKKFHEDVLIYILLRLPVKSLIRLKCISKTWYTLIQSSTFINLHL
NRTTTYNDELIFFKRSIKLEPDLFKNILSFLSSDNEDDLTPVYPDIDVPY
LTSDYCSRFHQLIGPCRGLIALTDFTVIVLLNPATRKYRLLPGSPFVCPK
GFTFVTRGVGFGYSTAENYYKLVRIFEVYTDPYDRDLDARHSKVEIYDSC
TDCWRDLDLTVKLLPKVRRFACSETFYKEAFHWCAHDDTVMILCFDIRLE
TFHYMKLPDHCHFWDNKGYGLTVLSNYLTFITYPNPRCALDPGQEFTDIW
IMEEYGANGTWIKKYTIGPLPIESSLSILKDHLLLLQSTSGTLSSYNLSS
DELKEFNFQGFISTLRLVVYKESLTIIPRESEHGTKVQTFoooooo
>C3
MPDGIIMKLHQDIIIYMLLRLPVKFLLRFKCISKYCYTLTKSSTFINIHL
NRATTSEDEYILFKRSFKEDVERYKGIFSFLSSNNGDDLNSIFPDLDVPN
MTSLYSITQDKLIGPCHGLVAVMNVSSTILLNPATRKYRLLPSSPFGVPK
GFYRNIENGGFGFDAVVNDYKIFRISEVYTEDSFGYPEEGERKVEVYELG
IDVWRELDHVDQQLPKLFWMTSSMPYNGTYHWIITLSYEHRLILLCFDMS
TEIFRYMKTPNTRYFSSGTRHSLVLLNDCLSFMCHPFPGPEIDPTKDLID
IWMMKDYNIYESWINIYTIRILPIHEFPLAIWKDSLLFFQGKTGYLMSYN
LNTDEVKELSLNGCKRSMRAIVYTESLAPIPEGSESSTQVHNFooo
>C4
MMDGTMKKLPEDMRIYILLRLPVKSLTRFKCVTKSWHTLIQSFNFINFHL
NQKSTTKDEFILFRRSIKHPDGFSHVLSFLVDHEGKDDLDPICPDIDMPY
LTTGFASSTSHQFTGPTNGLILLTDSLNFLLLNPATRSYRLLPPNPFCCP
RGFLRLIYGVGFGYDSIQKTYKVIRVSRVYGDPPYNDRSEMSWESEVYDS
STDSWRQLANVDQELPGPYMHPYSELFYKGTFHWYAQGHMRLLLCFDINT
EIFHTMQVPKTCASRDEKCHSLVVFDECLTFICYPDPRRESSPVQETIEI
WIMQEYSISESWIKKYTIRPPPIESPLAIWKDRLLLLQDKSGVLIAYDLN
SDEVKEFKLHGHPESLRVIVYKESLTPIPIGSTQVERFoooooooo
>C5
MMADGVVKKLPKDVVNNITLKLPVKSLLRFKCVSQFWYAYIQSWTFIILH
RNCASSVNDEIILFKRSFKEEHDHFKSIMSFLSSGHDSDDFQHVSPDLEV
PYLTNTTSCTFHRFIGPCHGLIVLTDKVTAVLFNPATRNYRLLKPSPFGS
PLGFHRSINGIAFGFDSIANEYKIVRLAELRGEPPFYCYSMREWRVEVYE
LRIDSWREVENVDQQLPYVHWYPCAELFYKGTSHWFGNTNTVVILGFDMS
TETFRNIKMPNTCHFKDRKCYGLVVLNESLTLICYPYPGCEIDPAIDFME
IWIMKEYGVNDSWSKKYTIIPLAIESPLAIWKNHLLLLQSVTGHLISYNF
NFDEIKEFKLHGWPKSLRVKIYEESLTLIPKESEFNTAQYoooooo
>C6
MGDEIVEKLPKDIVIYIFLMVLVKSLVRFKCVSKDWYTLIQSSTFISLHF
NRTTTTTKDEYMLVKRSFKEESNRFRSVMSFLSGGLDDDDDLYPVSPDLD
VPFLTTTNSCTFHRIMGPCNGLIVLTDKITTVLFNPATRSYRLLQPGRFG
CPVGFHRSINGVGFGFDSVANSYKIVRIAEVNGEPPFYCYTMREWKVEIY
EFSVDAWREQDQVYRQLPNVFWYPCFEMFYKGASHWFAHANTIVILCFDI
ITETFRSIKFPNTCHFQDENCYSLVILNDSLTLICYPYPEKVVEYEKDFM
EIWIMMEYGVDESWIKKYSITPLSIETPLAVWKDHLLLLESRSGSLISYD
LNSGEVKELNLHCWPPSFRIAVYQESLTLIPEEREHSTKCPKILES
>C7
MADEIVIKLPKDVVMYILLKFPVKSLLRFKRVSRNLYTLIQSSIFINLHL
NRNITANDDLILFKRSLKEEPNLFRSIMSFLSSFHDDYNLHHVSPDLDVP
YLTNTGGCTFHRFMGPCHGLIVLTDCEETVLFNPSTRNYRLLQPSPYDSP
LGFHRSINGIAFGFDSIGNEYKIARLAELSGEPPFNCFTMKEWRVEVYEL
SIDSWREIENVDQQLPYVHWYPCGELFYKGASHWFGHANRARVILCFDMS
TETFRDIKMPNTCHYKDRKCYGLVVLNECLTLICYPYPGCVINPAIDFME
IWVMKEYGVSESWNMKYKITPLAIESPLAIWKDHLLLLQSISGYLISYDL
NTDEVKEFNLNGWPESLRVNVYKESLALIPKCEHNIHLSIoooooo
>C8
MVEGLLKTLPNDLTIYILLILPVKALMRLKCVSKTCYTLIQSSAFVDLHL
NRKTTSKDECILLKRSLEEGINRYKTSLSFLCGDDHDYLSPIIHDVDVTH
LTTNCNFCHDQLVGPCHGLIALMHSPTTVLFNPSTRKYKLLPPSPLRHLK
GFYRSMEGEGFGFDSIINNYKVVKISTIYKVDHFDYLEEIGRKVEVYDLS
TDSWRELDHVAQELTTLCCVECTQMFYKGACHWIATQDLDAFRILCFDMS
SEVFRSLKIPENCHLFEGPWCRLALIQESLTLIYYRYPDQSTAQGKDSSV
VWIMKDYSVHESWVKNYTITSVPIHSPLAVWKGYLLVFEGKSGCLMSYDL
ICNKIKELNFHGFPESLRALVYKDSLISIPIGSEHSAQVHRFoooo
>C9
MANGILKKLPEDLVFLILLTLPVKSLMRFKCIAKAWSILIQSTTFINRYV
NRKTNTKDEFVLFKRAIKDDEEEFINILSFFSGHDDVLTPLFPDIDVSYM
TSKCDCTFNPLIGPCDGLIALTDSIITIIFNPATRNFRVLPPSPFGCPKG
YHRSVEGVGFGLDTISNYYKVVRISEVYCEEADGYPGPKVSKIDVCDLSA
DSWRELDHVKLPSIYWVPCSGILYKEMVHWFATTDVMIILCFDMSTEMFR
NIKMPDTCSIITHELYYGLVILCESFTLIGYSNPISSVDPAHDRMHIWVM
MEYGVSESWIMKYTIRPLSIESPLAVWKNHILLLQSRSGLLISYDLNSGE
AKELNLHGFPDSLSVQVYKECLTSIPKGSEYSTKVQKFoooooooo
>C10
MTAMKKLPIDVVINILFRLPVKSLARFKCVTKSWYSLIQSADFINRHLNR
ATTITDEFILFKRSFKEQEGFRNVMSFLVGGAGEDDLDPVSPDVDVPYLS
TSYSCICHQLTGPCHGLILLTDSTNLVLLNPATRNYRLLPPSPFGIQRGF
YRSVAGVGFGYDSVHKTYKVVRISEVYGEPPFNCPSVMEWKGEVYNSSTD
SWRELDCVDQELPWPYNFAYSEIFYEGAFHWYAHKNVVLILCFDVNTETF
RTMEVPEPCASYDEKCHSLLVLDEFLTLFCYPDPRRESSPIQETIEIWTM
QEYRVNESWIKKHTIKSPPIESPLAIWKDRLLLFQDKSGILISYDLNSDE
VKEFKLDGYPATLRVIIYKESLTPIPKGSTQVQNFooooooooooo
>C11
MPDRIIMKLPQDVFIYILLRLPVKLLLRFRCVSKSCYELIQSSTFINIHL
HRTTTSEDEYILFKRSFKEDVESYKGIFSFYSSHNDDGDMNSIFPDLDIP
NMTSLYSIDYDKIIGPCHGLIAVMDSSSTILFNPSTRKYRLLPSSPFGIP
KGYYRSIDSGGFGFDSVVNDYKVFRISDVYTEDRYGYPEEGEIKVEVYEV
GIDIWRELDHVDQDLPRLFWLTSSMYYNGAYHWITTSNHEDELIILCFDM
STEIFRNINTPDTRQFSSGTCHSLVLLDKCLSFMCHPYLGPEIDPTTDLI
DIWMMKDYNVYESWTKKYTIRVLPIDESPLAVWKDSLLFFQGKSGYLMSY
GFKSEEVQEWNLHGCQKSMRAIVYKESLVPVPRGIQCSTQLRNIoo
>C12
MKMPHGIMKKLPEDVILCIFLRIPVKSLMRFKCVSKNYYTLLQSTTFVNF
HLNRTTTVKDEFILLKRSFKEDINQYKTIFSFLSGGVDHDYLNPIFPDFD
VPNMTDTQSIIFDQLIGPCNGLIALMDDLTTIIFNPSTRNFRLLPPSPFD
RPKGYHRSIKCLGFGFDSVVNDYKVVRISEFLKDDCYGYVQVEEENVEIY
ELGIDCWRELDHINQQFPTIFWVPCSQIFHMGTFHWIAQRVILCFNMSTE
IFQHIRMPDPCHNIRNHSLVILNQSLTLICYRSVAPTSDPIEDLMEIWIL
EDYGVFESWVMKYTIRSLPIKIPLAIWKDNLLLFQSRSGYLMVYDLRTDN
VKELNIHGCPESMRVTVYKENLTIIPSGSENKTPVHKFoooooooo
>C13
MADGIVKKLSEDVVIFIFFRLPVKSLLRFKFVSKSFFTLIQSSTFITLYL
YNTTSSRDEYVLLKRCFIQENNQYKTILSFLAGDDDDYLNPIFQDLDVTH
LTSTRNCDHDQLIGPCHGLMALMDTQTTILFNPSTRNYRPLRPSPFGCPQ
GFHRCIQAVGFGFDTVSNDYKVVRISIIYKVDYDDEYPEERDRKFEVYDL
GIDYWRELENLSQELTTFCVTHCSQMFYKGACHWIASLDIDAYIILCFDM
SSETFRSLKIPESCHIINGPTCRLALVHDTLTLIYYPYPETEIPVEKDVI
NIWFMKEYNVYESWIRKYTIRGLLIDSPLTVWKGYLLLYQSRSGCLMSYN
LNNKDVRELNFNGYTKSLRAIVYKDSLTSIPRESEHTKQVYKFooo
>C14
MLDGIMKHLPKDIAMYILLRFPVKSLLRFKFISKSWSTLIESSTFINIHL
KRATTTNNEFLLFSRSYREETEGFKNVLSILSGGNNDDLMPVVSDLEQPY
LTFTEYYLFNKLVGPCNGLIVLTDFEIIVLFNPATKNYMLIPPSPFVCPK
GFHRSFRGGVGFGFDSIVKDYKFVTISEVFKNSEWGPDEKEQKVEVYDMR
IDSWRDLNHVDLQLPTVYYYPCFEMLYNGAFHWYAINDRFDHVILSFDIS
TEIFHSIKMPATGKSSGGKKYCLIVLNESLTLICYPNPDCEMDPTKDSMD
IWIMMEYGAYESWTKKYIIKPLPIESPLTIWRDHLLLLQSKRGLLVSYDL
SSNEVKEFDLHGHPKSLRVLVYKESLISLPKRGCEHGTKFKNCooo
>C15
MLDGTMKELPQDVVIYILVMLPVKSLLRFKCSCKTFCNIIKSSTFINLHL
NYTTNVMDELVLLKRSFKTDEYNFYKSILSFLSSKEDYDFTPISTDVEIP
HLTTTSACVFHQLIGPCNGLIALTDSLTTIVFNPSTRKYRLIPPCPFGIA
RGFRRSISGIGFGFDADAKDYKVVRLSEVYKEPCDKEMKVDIYDFSVDSW
RELLGQEVPIVYWLPCAEILYKRNFHWFAFSDDVIILCFDMNTEKFHNMG
MPDACHFDDGKCYGLVILCKCMTLICYPDPMPSSPTEKLTDIWIMKEYGE
KESWIKRCSIRLLPESPLAGWKDEILLLQSKMGHLIAYDHNSDEVKELDL
HGLPTSLRVIIYRESLTPIPRSKDSIELEQFooooooooooooooo
CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=100, Nseq=15, Len=427 

C1              -------MKELPQDVVIYIFVMLPVKSLLRFKCTDKTFCHIIKSSTFINL
C2              --MVDGIMKKFHEDVLIYILLRLPVKSLIRLKCISKTWYTLIQSSTFINL
C3              --MPDGIIMKLHQDIIIYMLLRLPVKFLLRFKCISKYCYTLTKSSTFINI
C4              --MMDGTMKKLPEDMRIYILLRLPVKSLTRFKCVTKSWHTLIQSFNFINF
C5              -MMADGVVKKLPKDVVNNITLKLPVKSLLRFKCVSQFWYAYIQSWTFIIL
C6              --MGDEIVEKLPKDIVIYIFLMVLVKSLVRFKCVSKDWYTLIQSSTFISL
C7              --MADEIVIKLPKDVVMYILLKFPVKSLLRFKRVSRNLYTLIQSSIFINL
C8              --MVEGLLKTLPNDLTIYILLILPVKALMRLKCVSKTCYTLIQSSAFVDL
C9              --MANGILKKLPEDLVFLILLTLPVKSLMRFKCIAKAWSILIQSTTFINR
C10             ----MTAMKKLPIDVVINILFRLPVKSLARFKCVTKSWYSLIQSADFINR
C11             --MPDRIIMKLPQDVFIYILLRLPVKLLLRFRCVSKSCYELIQSSTFINI
C12             MKMPHGIMKKLPEDVILCIFLRIPVKSLMRFKCVSKNYYTLLQSTTFVNF
C13             --MADGIVKKLSEDVVIFIFFRLPVKSLLRFKFVSKSFFTLIQSSTFITL
C14             --MLDGIMKHLPKDIAMYILLRFPVKSLLRFKFISKSWSTLIESSTFINI
C15             --MLDGTMKELPQDVVIYILVMLPVKSLLRFKCSCKTFCNIIKSSTFINL
                       :  :  *:   : . . ** * *::   :      :*  *:  

C1              HLNH-TTNFNDELVLLKRSFETDEYNFYKSILSFLFAK--EDYDFKPISP
C2              HLNR-TTTYNDELIFFKRSIK-LEPDLFKNILSFLSSD--NEDDLTPVYP
C3              HLNR-ATTSEDEYILFKRSFK-EDVERYKGIFSFLSSN--NGDDLNSIFP
C4              HLNQ-KSTTKDEFILFRRSIK--HPDGFSHVLSFLVDH-EGKDDLDPICP
C5              HRNC-ASSVNDEIILFKRSFK-EEHDHFKSIMSFLSSG-HDSDDFQHVSP
C6              HFNRTTTTTKDEYMLVKRSFK-EESNRFRSVMSFLSGGLDDDDDLYPVSP
C7              HLNR-NITANDDLILFKRSLK-EEPNLFRSIMSFLSSF-HDDYNLHHVSP
C8              HLNR-KTTSKDECILLKRSLE-EGINRYKTSLSFLCGD--DHDYLSPIIH
C9              YVNR-KTNTKDEFVLFKRAIK-DDEEEFINILSFFSGH---DDVLTPLFP
C10             HLNR-ATTITDEFILFKRSFK--EQEGFRNVMSFLVGG-AGEDDLDPVSP
C11             HLHR-TTTSEDEYILFKRSFK-EDVESYKGIFSFYSSH-NDDGDMNSIFP
C12             HLNR-TTTVKDEFILLKRSFK-EDINQYKTIFSFLSGG-VDHDYLNPIFP
C13             YLYN-TTSSRDEYVLLKRCFI-QENNQYKTILSFLAGD--DDDYLNPIFQ
C14             HLKR-ATTTNNEFLLFSRSYR-EETEGFKNVLSILSGG--NNDDLMPVVS
C15             HLNY-TTNVMDELVLLKRSFKTDEYNFYKSILSFLSSK--EDYDFTPIST
                :      .  :: ::. *.      : :   :*:          :  :  

C1              DVEIPHLTTTA-ACICHRLIGPCNGLIVLTDSLTTIVFNPATLKYRLIPP
C2              DIDVPYLTSDY-CSRFHQLIGPCRGLIALTDFTVIVLLNPATRKYRLLPG
C3              DLDVPNMTSLY-SITQDKLIGPCHGLVAVMNVSSTILLNPATRKYRLLPS
C4              DIDMPYLTTGFASSTSHQFTGPTNGLILLTDSLNFLLLNPATRSYRLLPP
C5              DLEVPYLTNTT-SCTFHRFIGPCHGLIVLTDKVTAVLFNPATRNYRLLKP
C6              DLDVPFLTTTN-SCTFHRIMGPCNGLIVLTDKITTVLFNPATRSYRLLQP
C7              DLDVPYLTNTG-GCTFHRFMGPCHGLIVLTDCEETVLFNPSTRNYRLLQP
C8              DVDVTHLTTNC-NFCHDQLVGPCHGLIALMHSPTTVLFNPSTRKYKLLPP
C9              DIDVSYMTSKC-DCTFNPLIGPCDGLIALTDSIITIIFNPATRNFRVLPP
C10             DVDVPYLSTSY-SCICHQLTGPCHGLILLTDSTNLVLLNPATRNYRLLPP
C11             DLDIPNMTSLY-SIDYDKIIGPCHGLIAVMDSSSTILFNPSTRKYRLLPS
C12             DFDVPNMTDTQ-SIIFDQLIGPCNGLIALMDDLTTIIFNPSTRNFRLLPP
C13             DLDVTHLTSTR-NCDHDQLIGPCHGLMALMDTQTTILFNPSTRNYRPLRP
C14             DLEQPYLTFTE-YYLFNKLVGPCNGLIVLTDFEIIVLFNPATKNYMLIPP
C15             DVEIPHLTTTS-ACVFHQLIGPCNGLIALTDSLTTIVFNPSTRKYRLIPP
                *.: . ::        . : **  **: : .    :::**:* .:  :  

C1              CPFGIPRGFRRSIS-GIGFGFDSDANDYKVVRLSEVYKEPCDK------E
C2              SPFVCPKGFTFVTR-GVGFGYSTAENYYKLVRIFEVYTDPYDR-DLDARH
C3              SPFGVPKGFYRNIE-NGGFGFDAVVNDYKIFRISEVYTEDSFG-YPEEGE
C4              NPFCCPRGFLRLIY-GVGFGYDSIQKTYKVIRVSRVYGDPPYN-DRSEMS
C5              SPFGSPLGFHRSIN-GIAFGFDSIANEYKIVRLAELRGEPPFY-CYSMRE
C6              GRFGCPVGFHRSIN-GVGFGFDSVANSYKIVRIAEVNGEPPFY-CYTMRE
C7              SPYDSPLGFHRSIN-GIAFGFDSIGNEYKIARLAELSGEPPFN-CFTMKE
C8              SPLRHLKGFYRSME-GEGFGFDSIINNYKVVKISTIYKVDHFD-YLEEIG
C9              SPFGCPKGYHRSVE-GVGFGLDTISNYYKVVRISEVYCEEADG-YPGPKV
C10             SPFGIQRGFYRSVA-GVGFGYDSVHKTYKVVRISEVYGEPPFN-CPSVME
C11             SPFGIPKGYYRSID-SGGFGFDSVVNDYKVFRISDVYTEDRYG-YPEEGE
C12             SPFDRPKGYHRSIK-CLGFGFDSVVNDYKVVRISEFLKDDCYG-YVQVEE
C13             SPFGCPQGFHRCIQ-AVGFGFDTVSNDYKVVRISIIYKVDYDDEYPEERD
C14             SPFVCPKGFHRSFRGGVGFGFDSIVKDYKFVTISEVFKNSEWG--PDEKE
C15             CPFGIARGFRRSIS-GIGFGFDADAKDYKVVRLSEVYKEPCDK------E
                       *:        .** .:  : **.  :  .              

C1              MKVDIYDFSVDSWREL--LGQDVPFVFWFPCAEILYKRNFHWF---AFAD
C2              SKVEIYDSCTDCWRDLDLTVKLLPKVRRFACSETFYKEAFHWC---AHDD
C3              RKVEVYELGIDVWRELDHVDQQLPKLFWMTSS-MPYNGTYHWIITLSYEH
C4              WESEVYDSSTDSWRQLANVDQELPGPYMHPYSELFYKGTFHWY---AQGH
C5              WRVEVYELRIDSWREVENVDQQLPYVHWYPCAELFYKGTSHWF---GNTN
C6              WKVEIYEFSVDAWREQDQVYRQLPNVFWYPCFEMFYKGASHWF---AHAN
C7              WRVEVYELSIDSWREIENVDQQLPYVHWYPCGELFYKGASHWF---GHAN
C8              RKVEVYDLSTDSWRELDHVAQELTTLCCVECTQMFYKGACHWI---ATQD
C9              SKIDVCDLSADSWRELDHV--KLPSIYWVPCSGILYKEMVHWF---ATTD
C10             WKGEVYNSSTDSWRELDCVDQELPWPYNFAYSEIFYEGAFHWY---AHKN
C11             IKVEVYEVGIDIWRELDHVDQDLPRLFWLTSS-MYYNGAYHWITTSNHED
C12             ENVEIYELGIDCWRELDHINQQFPTIFWVPCSQIFHMGTFHWI---AQR-
C13             RKFEVYDLGIDYWRELENLSQELTTFCVTHCSQMFYKGACHWI---ASLD
C14             QKVEVYDMRIDSWRDLNHVDLQLPTVYYYPCFEMLYNGAFHWY---AIND
C15             MKVDIYDFSVDSWREL--LGQEVPIVYWLPCAEILYKRNFHWF---AFSD
                 . :: :   * **:       ..           :    **        

C1              VV--VILCFEMNTEKFHNMGMPDACH-FADGKCYGLVILFKCMTLICYPD
C2              TV--MILCFDIRLETFHYMKLPDHCH-FWDNKGYGLTVLSNYLTFITYPN
C3              RL--ILLCFDMSTEIFRYMKTPNTRY-FSSGTRHSLVLLNDCLSFMCHPF
C4              MR--LLLCFDINTEIFHTMQVPKTCA-SRDEKCHSLVVFDECLTFICYPD
C5              TV--VILGFDMSTETFRNIKMPNTCH-FKDRKCYGLVVLNESLTLICYPY
C6              TI--VILCFDIITETFRSIKFPNTCH-FQDENCYSLVILNDSLTLICYPY
C7              RA-RVILCFDMSTETFRDIKMPNTCH-YKDRKCYGLVVLNECLTLICYPY
C8              LDAFRILCFDMSSEVFRSLKIPENCH-LFEGPWCRLALIQESLTLIYYRY
C9              VM--IILCFDMSTEMFRNIKMPDTCSIITHELYYGLVILCESFTLIGYSN
C10             VV--LILCFDVNTETFRTMEVPEPCA-SYDEKCHSLLVLDEFLTLFCYPD
C11             EL--IILCFDMSTEIFRNINTPDTRQ-FSSGTCHSLVLLDKCLSFMCHPY
C12             ----VILCFNMSTEIFQHIRMPDPCH---NIRNHSLVILNQSLTLICYRS
C13             IDAYIILCFDMSSETFRSLKIPESCH-IINGPTCRLALVHDTLTLIYYPY
C14             RFDHVILSFDISTEIFHSIKMPATGK-SSGGKKYCLIVLNESLTLICYPN
C15             DV--IILCFDMNTEKFHNMGMPDACH-FDDGKCYGLVILCKCMTLICYPD
                     :* *::  * *: :  *             * :. . :::: :  

C1              PMPS-SPTEKLTDIWIMKEYGEKESWIKRCSIRLLP--ESPLAVWKDEIL
C2              PRCALDPGQEFTDIWIMEEYGANGTWIKKYTIGPLPI-ESSLSILKDHLL
C3              PGPEIDPTKDLIDIWMMKDYNIYESWINIYTIRILPIHEFPLAIWKDSLL
C4              PRRESSPVQETIEIWIMQEYSISESWIKKYTIRPPPI-ESPLAIWKDRLL
C5              PGCEIDPAIDFMEIWIMKEYGVNDSWSKKYTIIPLAI-ESPLAIWKNHLL
C6              PEKVVEYEKDFMEIWIMMEYGVDESWIKKYSITPLSI-ETPLAVWKDHLL
C7              PGCVINPAIDFMEIWVMKEYGVSESWNMKYKITPLAI-ESPLAIWKDHLL
C8              PDQSTAQGKDSSVVWIMKDYSVHESWVKNYTITSVPI-HSPLAVWKGYLL
C9              PISSVDPAHDRMHIWVMMEYGVSESWIMKYTIRPLSI-ESPLAVWKNHIL
C10             PRRESSPIQETIEIWTMQEYRVNESWIKKHTIKSPPI-ESPLAIWKDRLL
C11             LGPEIDPTTDLIDIWMMKDYNVYESWTKKYTIRVLPIDESPLAVWKDSLL
C12             VAPTSDPIEDLMEIWILEDYGVFESWVMKYTIRSLPI-KIPLAIWKDNLL
C13             PETEIPVEKDVINIWFMKEYNVYESWIRKYTIRGLLI-DSPLTVWKGYLL
C14             PDCEMDPTKDSMDIWIMMEYGAYESWTKKYIIKPLPI-ESPLTIWRDHLL
C15             PMPS-SPTEKLTDIWIMKEYGEKESWIKRCSIRLLP--ESPLAGWKDEIL
                         .   :* : :*    :*     *      . .*:  :. :*

C1              LLHSKTGHLIAYDFNSNEVQELDLHGYPESLRIIIYRESLTAIP--RNND
C2              LLQSTSGTLSSYNLSSDELKEFNFQGFISTLRLVVYKESLTIIP-RESEH
C3              FFQGKTGYLMSYNLNTDEVKELSLNGCKRSMRAIVYTESLAPIP-EGSES
C4              LLQDKSGVLIAYDLNSDEVKEFKLHGHPESLRVIVYKESLTPIP-IGSTQ
C5              LLQSVTGHLISYNFNFDEIKEFKLHGWPKSLRVKIYEESLTLIP-KESEF
C6              LLESRSGSLISYDLNSGEVKELNLHCWPPSFRIAVYQESLTLIP-EEREH
C7              LLQSISGYLISYDLNTDEVKEFNLNGWPESLRVNVYKESLALIP--KCEH
C8              VFEGKSGCLMSYDLICNKIKELNFHGFPESLRALVYKDSLISIP-IGSEH
C9              LLQSRSGLLISYDLNSGEAKELNLHGFPDSLSVQVYKECLTSIP-KGSEY
C10             LFQDKSGILISYDLNSDEVKEFKLDGYPATLRVIIYKESLTPIP-KGSTQ
C11             FFQGKSGYLMSYGFKSEEVQEWNLHGCQKSMRAIVYKESLVPVP-RGIQC
C12             LFQSRSGYLMVYDLRTDNVKELNIHGCPESMRVTVYKENLTIIP-SGSEN
C13             LYQSRSGCLMSYNLNNKDVRELNFNGYTKSLRAIVYKDSLTSIP-RESEH
C14             LLQSKRGLLVSYDLSSNEVKEFDLHGHPKSLRVLVYKESLISLPKRGCEH
C15             LLQSKMGHLIAYDHNSDEVKELDLHGLPTSLRVIIYRESLTPIP--RSKD
                . ..  * *  *.    . :* .:.    ::   :* : *  :*      

C1              CIELQNFRCNooooooooooooooooo
C2              GTKVQTFoooooo--------------
C3              STQVHNFooo-----------------
C4              VERFoooooooo---------------
C5              NTAQYoooooo----------------
C6              STKCPKILES-----------------
C7              NIHLSIoooooo---------------
C8              SAQVHRFoooo----------------
C9              STKVQKFoooooooo------------
C10             VQNFooooooooooo------------
C11             STQLRNIoo------------------
C12             KTPVHKFoooooooo------------
C13             TKQVYKFooo-----------------
C14             GTKFKNCooo-----------------
C15             SIELEQFooooooooooooooo-----
                                           




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] 	input.prot.fasta.muscle_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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 15 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C15 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  396 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 15 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C15 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  396 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 15 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C15 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  396 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 15 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C15 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  396 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 15 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C15 Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  396 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  396 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 15 SEQUENCES  [PROTEIN]
  Input File in