--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 27 18:54:56 GMT 2020
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=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/opt/mrbayes_3.2.2/src
tcoffee.dir=
tcoffee.minScore=3
input.fasta=
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/data/14_chinensisF_box_results/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/14_chinensisF_box_results/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)

(Values are saved to the file /data/14_chinensisF_box_results/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -16154.70        -16170.26
2     -16153.35        -16170.12
--------------------------------------
TOTAL   -16153.81        -16170.19
--------------------------------------


Model parameter summaries over the runs sampled in files
"/data/14_chinensisF_box_results/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/14_chinensisF_box_results/Muscle/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 "/data/14_chinensisF_box_results/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         4.828005    0.020328    4.558574    5.117780    4.825326   1264.12   1382.56    1.000
r(A<->C){all}   0.141636    0.000097    0.122858    0.161245    0.141586    885.72    898.01    1.000
r(A<->G){all}   0.260340    0.000169    0.235220    0.285249    0.260207    753.31    778.59    1.001
r(A<->T){all}   0.108632    0.000053    0.094680    0.122935    0.108519   1112.91   1148.01    1.000
r(C<->G){all}   0.161374    0.000125    0.139094    0.182122    0.161395    682.10    775.50    1.000
r(C<->T){all}   0.244971    0.000151    0.222628    0.270091    0.244758    863.65    878.43    1.001
r(G<->T){all}   0.083047    0.000051    0.069028    0.096911    0.082861    963.05   1020.84    1.001
pi(A){all}      0.286487    0.000059    0.270769    0.300724    0.286459    752.93    808.69    1.000
pi(C){all}      0.184927    0.000038    0.172744    0.196798    0.184896    747.96    767.37    1.001
pi(G){all}      0.218478    0.000050    0.204502    0.232092    0.218268    817.87    872.48    1.000
pi(T){all}      0.310108    0.000069    0.293498    0.325894    0.309912    904.38   1052.51    1.000
alpha{1,2}      1.363420    0.021079    1.090982    1.647462    1.348588    997.47   1106.28    1.000
alpha{3}        4.681634    0.681732    3.312281    6.492241    4.601259   1449.92   1475.46    1.000
pinvar{all}     0.023269    0.000157    0.001170    0.046502    0.022239    772.44    907.16    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	-7699.732033
Model 2: PositiveSelection	-7692.990556
Model 0: one-ratio	-7842.927958
Model 3: discrete	-7673.668478
Model 7: beta	-7688.744247
Model 8: beta&w>1	-7675.730305


Model 0 vs 1	286.39185

Model 2 vs 1	13.482954000000973

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: Rchinensis_NC_037090F_box_minus3)

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

    48 S      0.796         2.122
    57 R      0.764         2.077
    62 D      0.871         2.227
    85 H      0.704         1.992
    95 S      0.823         2.160
   124 N      0.528         1.744
   128 P      0.721         2.017
   130 G      0.657         1.925
   131 T      0.691         1.974
   148 D      0.903         2.273
   174 M      0.582         1.820
   178 F      0.816         2.150
   179 T      0.592         1.834
   190 I      0.869         2.224
   211 Y      0.944         2.330
   226 W      0.786         2.108

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: Rchinensis_NC_037090F_box_minus3)

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

    48 S      0.760         2.207 +- 0.743
    57 R      0.711         2.115 +- 0.758
    62 D      0.843         2.347 +- 0.677
    85 H      0.687         2.112 +- 0.838
    95 S      0.795         2.272 +- 0.738
   128 P      0.683         2.083 +- 0.790
   130 G      0.644         2.043 +- 0.852
   131 T      0.654         2.041 +- 0.819
   148 D      0.901         2.464 +- 0.651
   174 M      0.537         1.846 +- 0.826
   178 F      0.790         2.265 +- 0.738
   179 T      0.561         1.897 +- 0.849
   190 I      0.845         2.352 +- 0.676
   211 Y      0.944         2.532 +- 0.578
   226 W      0.757         2.208 +- 0.758


Model 8 vs 7	26.027883999999176

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: Rchinensis_NC_037090F_box_minus3)

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

    48 S      0.938         1.605
    54 C      0.708         1.405
    56 L      0.571         1.278
    57 R      0.922         1.591
    59 I      0.621         1.326
    60 N      0.662         1.367
    62 D      0.964*        1.627
    64 K      0.670         1.370
    74 S      0.746         1.435
    85 H      0.885         1.559
    92 L      0.676         1.376
    95 S      0.947         1.613
   108 L      0.785         1.474
   124 N      0.863         1.541
   128 P      0.897         1.569
   129 N      0.604         1.308
   130 G      0.866         1.543
   131 T      0.895         1.568
   148 D      0.958*        1.622
   150 G      0.660         1.362
   174 M      0.854         1.533
   178 F      0.940         1.606
   179 T      0.838         1.519
   190 I      0.960*        1.624
   194 S      0.656         1.353
   211 Y      0.973*        1.635
   225 H      0.541         1.255
   226 W      0.933         1.601

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: Rchinensis_NC_037090F_box_minus3)

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

    48 S      0.928         1.465 +- 0.207
    51 C      0.553         1.170 +- 0.385
    54 C      0.742         1.325 +- 0.315
    56 L      0.631         1.237 +- 0.359
    57 R      0.913         1.453 +- 0.219
    59 I      0.674         1.271 +- 0.344
    60 N      0.715         1.305 +- 0.321
    62 D      0.955*        1.485 +- 0.180
    64 K      0.711         1.299 +- 0.330
    74 S      0.763         1.337 +- 0.315
    85 H      0.877         1.429 +- 0.253
    90 F      0.521         1.159 +- 0.369
    92 L      0.716         1.304 +- 0.328
    95 S      0.939         1.473 +- 0.196
   107 V      0.542         1.171 +- 0.372
   108 L      0.802         1.370 +- 0.288
   124 N      0.864         1.416 +- 0.247
   126 C      0.506         1.137 +- 0.382
   128 P      0.888         1.435 +- 0.243
   129 N      0.646         1.249 +- 0.359
   130 G      0.860         1.415 +- 0.268
   131 T      0.888         1.436 +- 0.239
   147 V      0.570         1.187 +- 0.376
   148 D      0.947         1.480 +- 0.193
   150 G      0.701         1.294 +- 0.334
   174 M      0.853         1.409 +- 0.264
   178 F      0.930         1.467 +- 0.207
   179 T      0.838         1.399 +- 0.276
   190 I      0.950*        1.482 +- 0.186
   194 S      0.693         1.282 +- 0.344
   206 L      0.524         1.148 +- 0.386
   211 Y      0.963*        1.491 +- 0.177
   225 H      0.617         1.229 +- 0.356
   226 W      0.924         1.462 +- 0.211

>C1
MSEEIMVSILSILPPKSVMRFKCVRKSWYSLINNSSFIAKHLSNTMCNKH
STSILCKSCVLRDINTDEKEVVCSLISLSSNSNNDEHHIHSAVEDIHIPL
SFGVTTRGQFKGDEVLLAVSIIGHCDGIICLVASLNIVLWNPAIKEFKIL
PNQCLPNGTLNSMAFGYDPKSKDYKFLNIVDPSEETLGEHRIVYDFPRIE
VYTLSTDSWREMKTYSLETETTMFLCFTKLYFNGFCYWIGCEKQKDFMDY
FDRDDEEWVRQVIHSFDMSTEVFDHILLPNSLYLYEPLALYFNMHVILWN
ESIALFGLYHWRSooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooo
>C2
MAGCKLPRVMVVQILSRMPPKSLMRFKCVHKSWNSLISSRHVVAKHLQFH
NHLSSSTTILLRRPVIWRTETKNEEIVFSLLTLRNENNGDEDNLDYDIED
IHFPPSIGLKTRAQFIENPGPTYECADIVGHCGGIICLSLYAAGDLVLYN
PAIKEFKVIPEPCLPRPRQFYFRCDAFGYDPKSEDYILVNVASYGENRYD
DDRLVIEPLRAEMYTLGTNSWREINIHNLETETTMFRPNHFQVYFKGNCY
GLAEEIKKEFISSFDSLEEYYIREVIVWFNTSDRVFHSALTPDCLYRYPA
HDFNLTVWNNCVALFGYNRCGSKPFEIWVMGESDGFTCSWIKHLSVDITE
SPQPLVLWESNQSLLVSPRIRVALYSFATKTFKYLPLCAAEHFDAIPFVN
SIVPLNRDLVSVNISooooooooooooooooooooooooooooooooooo
ooooooooooooooo
>C3
MAEFCKMPEEMVVPILSRLLPKSLMRFKCIHKSWHSLINSPQFISKHLHF
HNNLSSSTTILLKRPVMRRTDTLNEKIVCSFLNLHNANDGDEDNLHYDIK
DLEFQPSMGLNTRGQFIEIPNEYYYNCAYIIGQCDGIFCLTLYAAKDLVL
YNPAIKEFKFLPESCLQDKNIGSVGFGYDPKSEDYILVSVVSYGHGEQYY
NDDRLVIDPMRAEVYTMSTDCWREIKIHNLETETTFFWPRHFQVYFKGNC
YWLAHEKRKEFITLYDRLEEYYIWEAIVCFDTANRIFHNILVPDCLYEFP
MHDLDLAVWHDSIALFGFYRGGSRPFEIWVMDNFDGLNSSWVKQLSVDIA
KSPIPLALWERNKILLVFTHTQIALYSFVTETYQYLPLYGASFFRLFLMW
IVoooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooo
>C4
MVEFCKISEEIVMQILSRTPPKSLMRFKCIQKSWNSMINDPQFAAKHLHF
YNNPSSSTAFLVKRPVILRSETSNENVVLSYLRLETYTNGDDEDLHFVVE
DIICPPFKGLKARGQFIELPRRDDSVYIISHCDGIIFLTLYTGDLFLYNP
AIKEFKIILASCCHDCCWSTVGFGYDLKCKDYIILEIACYGETNYNDPQR
LVVDPPIAAVYTLGIDSWREIKTDHLQTEDTYFWPTAFDLYSKGIFYLFG
YEEKKEFLDDMERCEETNKQVMILYDTRDELFHIAMLPDSFNEPACGVHD
IHVALLNKSIALYGFSIFESIHSIQIWVTDDIRGAQEYSWTKYLSLNPVD
NVRRSLAFWKIDEVLMIAKDGRVVLCNLLTGKLKYFPIHGLHLGDDIQGI
VCVDSIVPLNGRELSRHooooooooooooooooooooooooooooooooo
ooooooooooooooo
>C5
MSEFSKFPEEMALHILSRMPPKSLMRFKCVRKSWYVLINNPSFVAKHLYN
SLHNKQSTCIFCKRYVFRDIATKDVESVVSLITFSDDDVGDTNHEHISHS
VIQDIDLPLSMSGIPKNHLNEPELLGAVYITGHCDGIICLVHGEIVLWNP
AIKQFKILPKPLLTNGIVNSIGFGYDARSKDYKVFSFPTHDEDRSSERDF
NYPPHVEVYSLSTDLWTEINADHLETETTNLYPEFFQMYFKGIWYWTGSE
QQKEFMVVYDSMDEEWVRQLIIVFDMNDEVFEDILFPYSLYGPMIPYLEM
RVIVWNESVALFGQYRFGYADDAFGLWVMDDIVKGSWTKQLTLEVVVGTR
MTLEMWKSDEILMVANDNRIFSYNIRTEEIKYLPIESTHPTFSAAIVCIN
SIVPVIHGRQQAoooooooooooooooooooooooooooooooooooooo
ooooooooooooooo
>C6
MANFSKLYSSEDLVEQILSGLPPKSLMRFKCVCDLWCNLIKSPSFVAKHL
SGSMRASSMPVLFKRPVPRDKENNIMDEKGVENDDDDVGTLLWSLNLCNE
DDNDYLLSTVLEELNVPLPAPLKLKHSSDLTIAGHCDGIICLKLFTGNVI
LCNPAMKEFKLLPKSFLLLCNDDFDDLWSLSYELRYYTEQLGFGYDPEGK
DYKVLRFVIYDESCYWFKAEVYTMDSNSWREIKTEYNNIIQFVNWSSDQP
IYFNGICYWQVSGSRGEFILSFDMGNELFHEILNPDLPDKCGVVRLAVWK
EFISLFTYQEEIVVPPSYDMWVMMDDLGDGKGSWTKYFTIGPVEGDKWPL
LFWKGDQLLMESNDGQIVLYNIGTQILKYLPIHFIRDLYYSQELVYVNSI
VSINGGNVLEDIHISAFYGNGKFYSINKGDVIDISAFYGITSoooooooo
ooooooooooooooo
>C7
MAELICKMPEEMTLQFLSRLPPKSLMRFKCIHKSWYALINNPKFIDKHLH
LYNKDSYTCFLLKRSVVARTQSIKEEILFSFLYVPNDNDDEDSHPHCVVE
DIYFPTAMGLKTKGHNIELPGSYGGETIYILGHCDGIICLVYHSGGLVFY
NPSIREFKIIPPSCLTESFSCVGGFGYDPKCKDYKVVNIVPSGEDSYDHN
QRLVIYPPRAEVYTLSTDSWRQIKIDYLETETTSFWPDIYQMCYKGVFYW
LGHEQDKEYLCYYDRLSSPSIRDVILLYDTGEEVFRTRLLPDSFKDLGLH
ALSMSLTMWNGSIALFGFSYWGPDIESFKIWMMDDFGSWTKHLTYETIMG
IYLSLVLWRSDDVLMVANDGRIVSYSLSRDRVKYFPIQGVWGTYQAFVCV
NSNSIVSVKGGNKVESRDIQTSNVLLoooooooooooooooooooooooo
ooooooooooooooo
>C8
MAELSKFAEEIMVEIMSRLPPKSLMRFKCVRRSWNALINNPNFAAKHLAS
SKRTLLSSSSTTIIFRHFLIADLNPDEMEMILSLYNFCNDFDGCFLEDIH
FPHSMGLECRRKFHEPGSTFGISCYCDGIICLADYGQKPNIVLCNPAIKE
FKLLSESQLALSSPTFRKTAAVGFGCDLMLKNYKVVRLINSGWRYRDDQD
TVIPHLYAEVYNLRTDSWKEIKIDGLLKENKIVVPDSNAQTKGLCSKGIL
YWCAMEEEKVLEVTCDGDDEQKEIDMHACIISFNVGDESFHVINIGSYDD
HCCLIDGVLGLWKESIALCVRGWTTLDIWVMDDFGGGKGSWTKYLAIEPV
VKITSQFALFGKSDEQFVLVACDDSVVIFYDICTNKFNYLPLNGVLLHHT
QVVEYASSIVSVKECNKLDMEAoooooooooooooooooooooooooooo
ooooooooooooooo
>C9
MENFSKLSEEMVVRILSRLPPKSLIRFRCVRKLWYNVINSPNFVAKNLTT
SKHNKFSSSTCILAKHTVLKDSNIKDRNEILEVLRDNSIETKKILLSLCN
LCNDNDGDDPNLNYVVDDFTVPLPLGLLPFSLEIAGHCDGIICLNNSFLD
DIVLCNPATKESKLLPKSCLLLPPRHPNDYDEIESDVNAVGFGYDSKAQE
YKVVRIVSFITGVHKPLPSKAEVYTIGTNSWREIKDQTESHVFWAASFKL
FLKGFYFWWASICPPEQEIILSFDMNEELFHDIYIPESVRHDIVRCNRGL
AVWKESIALLAYGGDSGAQSFDIWVIDDFGVFKSSWIKYLTIGPLEGISI
PLIFWKSNEFLMAATDGRLVSYNLSTQMFKYLPIHGVEDPPYIQAVVYVN
SIVSVHASNKLEGINNSSoooooooooooooooooooooooooooooooo
ooooooooooooooo
>C10
MGKLCKLSEEMVGQFLSRLPPKALMRFKCIHKSWYNLITSPSFIAKNLSN
SKNNKFASTTRILFKRTVLKDIKDKNEIFYVLRDNNNDRRYIFLSLLDLC
NDNDGDDQNLHSVVDDLIVPLPFSICPFSLQIAGHCDGLICLVNIVNEEV
ALCNPAIKEFKFLPRSSLLLPRRHPEDDDGIESDVNAVGFGYDSKTQDYK
IVRVITYITGIAYTLPSKAEVYTLSSHSWREIKIDKECHVFWTPSFEIHF
RGIYYWSALTYPTPGADKEAIFAFDMSEETFEEIPIPDGICARDGIIKFL
AVWKESVALISCIGDGPKSFDIWVMDDSSGIKGSWTKHLVIGPIECEIPL
VFWKSDELLLVISDGRVVSYHLGNKTIKYLPIHGVEDPQYIHAVVCVNSM
ISVKKTKGoooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooo
>C11
MMQSSKLAEEIVVQFMSRLPPKALMRFKCIRKSWYNLINSPSFVAQNLSY
SMNNKFTSSTCILSKHTVLKDGNITDRNEILDILTYGNNDKQQILLSLLN
LCNDHNGDDQELFSVIKDNFIVPFPFDKCSLSLKIAGHCDGIICLVNVED
VALCNPSIKEFNHLPKSCLLLPPKNWDDYENEDDYYEALESESNAVGFGY
DSKANVYKVVRIVQFTSGYVFTSHPSRVEVYTLGANCWREIKADVLVSTV
CWSPSFEMYFKGIYYWDAYSYLTPRQYKDGILAFDMSDELFYLIYHPETT
REFNKSLAVWKESIALITYEGDAPKCFDLWLNEDSSCFKGLWTKYFTIGP
VEVEIPLVFWKSNEILMVNADKHIVSYNLDTQTLKCLPMHGVEDPEYIYA
IIYVSSIISVNRDNKLECTTTSIooooooooooooooooooooooooooo
ooooooooooooooo
>C12
MTEFCKIPEAMGLQILSRLPPKSLMRFKCVHKSWHTLMKDPNFVAKHLSN
SMHDNFCRTTGVLFKRENFKDTGTAERQSESLLSLINFCNANGDGEHDIH
CLVEDVTKGQFSGFEVLESAWIIGHCHGIICLRNATKIILWNPAIREVKV
TSPYVPDENLSDLGIGYDPKSDTYKVVHISYGTQEEYGDGHILIDRPKTE
VYTLGTDSWRQIMTGCLETETTHFWFQDFHMYFNGFCYWNGREQLKEYQN
FYDLQEEHHIRPVIISFDMGDEVFHNMLLPDFVYETYMWSYVLRLMAWNE
SVAIFGLDHGITSHESWGLWVMDDFGGVTGSWIKQFSFVSAVGFLDTPLQ
IWKSDEILIVSKERRVVSYNLDTEQYKYLPIHSMDSDYFEAVVYMNSIVS
VNGSKToooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooo
>C13
MALEKDSEIAELTESGKNIAQDVVEQILSTLPPKSLMRFKCVSKWWYHLI
TSPRFVAKHLSISKHNRPSTCALIKSLVSNDAEAQEPEMVFSLLNFSYEN
DNNAGGALSTNLSSVEDLTIPTRVVESLRIIGHCDGIVCLALIDYQQRLA
KPSQVCLWNPAIQQFKFLPEEPFLPDWSKVPHSRMVQEFAYLRPISLLNG
ETMGFGYDPKSKDYKVIDIGFSDSKFYGDPECYGGHVIVYPPKAVVYTLQ
TDSWREIKTFSLERETSYLWPDTFQLYLKGVCYWLGYEQQKEFLCLFQTH
QEEEERIARAIISFDTSDEVFHDIMLPHGLLEFYGFDNFLTLHLTEWNES
VALFSLLFEDEHKATMWVMDAKGAWTKQLTFEYVDYFPYSLPRKILAFWK
SNEIFGVGENGSIVCYNLNTKIVKHLPIRSVPDYFPPSRDTFYPFCCIAY
VNSVVPIMNHVREHI
>C14
MTLEFGKTIDEDVVEQILSTLPPKSLKRFQCVSNRWHALITTPRFVAKHL
SISRHNNLSTSVLMKRKVHEDTNSDETQEFFSFLHFRNDEDNDVDGVHDE
HSFLSSIQEFHIPFSTGVKTWAEALIIIGHCNGIICLAQAVSGEVIICNP
AIHEYKLLPPSPYLPDSDWPYSAIFRFRDGLGFGYDPNFNEYKIVNIGFP
APELSTPDGYNIYNPPKAAVYTLGTDAWRKIKTDTLETETTILWPQIFQM
HFKDMCFWLAPEQHKELDVLDEDEEQFIREVIVMFDTGDELFHNIMLPDE
FDYPSKNYFVPNLLVWKDSVALLGIQISQFSSYGIWVIDEFGGHNGGAWT
KHITFELPVEPLIFWKSDRVLLNDPNDTDYRGLILDYNLDTKKLKNLPVQ
SERSDSSAIVYVSSIVSVLGGSKPKNKDNSTPNVoooooooooooooooo
ooooooooooooooo
CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=99, Nseq=14, Len=587 

C1              -----------M---------SEEIMVSILSILPPKSVMRFKCVRKSWYS
C2              -----------MAG--CKL--PRVMVVQILSRMPPKSLMRFKCVHKSWNS
C3              -----------MAEF-CKM--PEEMVVPILSRLLPKSLMRFKCIHKSWHS
C4              -----------MVEF-CKI--SEEIVMQILSRTPPKSLMRFKCIQKSWNS
C5              -----------MSEF-SKF--PEEMALHILSRMPPKSLMRFKCVRKSWYV
C6              -----------MANF-SKLYSSEDLVEQILSGLPPKSLMRFKCVCDLWCN
C7              -----------MAELICKM--PEEMTLQFLSRLPPKSLMRFKCIHKSWYA
C8              -----------MAEL-SKF--AEEIMVEIMSRLPPKSLMRFKCVRRSWNA
C9              -----------MENF-SKL--SEEMVVRILSRLPPKSLIRFRCVRKLWYN
C10             -----------MGKL-CKL--SEEMVGQFLSRLPPKALMRFKCIHKSWYN
C11             -----------MMQS-SKL--AEEIVVQFMSRLPPKALMRFKCIRKSWYN
C12             -----------MTEF-CKI--PEAMGLQILSRLPPKSLMRFKCVHKSWHT
C13             MALEKDSEIAELTESGKNI--AQDVVEQILSTLPPKSLMRFKCVSKWWYH
C14             ----------MTLEFGKTI--DEDVVEQILSTLPPKSLKRFQCVSNRWHA
                                      . :   ::*   **:: **:*:   *  

C1              LINNSSFIAKHLSNTMCNK--HS---TSILCKSCVLRDINTDEK------
C2              LISSRHVVAKHLQ--FHNHLSSS---TTILLRRPVIWRTETKNE------
C3              LINSPQFISKHLH--FHNNLSSS---TTILLKRPVMRRTDTLNE------
C4              MINDPQFAAKHLH--FYNNP---SSSTAFLVKRPVILRSETSNE------
C5              LINNPSFVAKHLYNSLHNK--QS---TCIFCKRYVFRDIATKDV------
C6              LIKSPSFVAKHLSGSMR-A--SS---MPVLFKRPVPRDKENNIM---DEK
C7              LINNPKFIDKHLH--LYNK-DSY---TCFLLKRSVVARTQSIKE------
C8              LINNPNFAAKHLASSKRTLL--SSSSTTIIFRHFLIADLNPDEM------
C9              VINSPNFVAKNLTTSKHNKFSSS---TCILAKHTVLKDSNIKDRNEILEV
C10             LITSPSFIAKNLSNSKNNKFAST---TRILFKRTVLKDIKDKNE--IFYV
C11             LINSPSFVAQNLSYSMNNKFTSS---TCILSKHTVLKDGNITDRNEILDI
C12             LMKDPNFVAKHLSNSMHDNFCRT---TGVLFKRENFKDTGTAER------
C13             LITSPRFVAKHLSISKHNR--PS---TCALIKSLVSNDAEAQEP------
C14             LITTPRFVAKHLSISRHNN--LS---TSVLMKRKVHEDTNSDET------
                ::.   .  ::*                 : :                  

C1              ---------EVVCSLISLSSNSNND-----EHH-IHSAV-EDIHIPLSFG
C2              ---------EIVFSLLTLRNENNGD-----EDN-LDYDI-EDIHFPPSIG
C3              ---------KIVCSFLNLHNANDGD-----EDN-LHYDI-KDLEFQPSMG
C4              ---------NVVLSYLRLETYTNGD-----DED-LHFVV-EDIICPPFKG
C5              ---------ESVVSLITFSDDDVGDTN---HEHISHSVI-QDIDLPLSMS
C6              GVENDDDDVGTLLWSLNLCNEDDND-------YLLSTVL-EELNVPLPAP
C7              ---------EILFSFLYVPNDNDDE-----DSH-PHCVV-EDIYFPTAMG
C8              ---------EMILSLYNFCNDFDG------------CFL-EDIHFPHSMG
C9              LRDNSIETKKILLSLCNLCNDNDGD-----DPN-LNYVV-DDFTVPLPLG
C10             LRDNNNDRRYIFLSLLDLCNDNDGD-----DQN-LHSVV-DDLIVPLPFS
C11             LTYGNNDKQQILLSLLNLCNDHNGD-----DQE-LFSVIKDNFIVPFPFD
C12             -------QSESLLSLINFCNANGDG-----EHD-IHCLV-EDVTKGQFSG
C13             ---------EMVFSLLNFSYENDNNAGGALSTN-LSSV--EDLTIPTRVV
C14             ---------QEFFSFLHFRNDEDNDVDGVHDEHSFLSSI-QEFHIPFSTG
                           .     .     .                .:.       

C1              VTTRGQFKGDEVL---LAVSIIGHCDGIICLV-AS---------LNIVLW
C2              LKTRAQFIENPGP-TYECADIVGHCGGIICLS-LY-------AAGDLVLY
C3              LNTRGQFIEIPNEYYYNCAYIIGQCDGIFCLT-LY-------AAKDLVLY
C4              LKARGQFIELPRR--DDSVYIISHCDGIIFLTL---------YTGDLFLY
C5              GIPKNHLNEPELL---GAVYITGHCDGIICLV-H----------GEIVLW
C6              LKLKHS----------SDLTIAGHCDGIICLKL---------FTGNVILC
C7              LKTKGHNIELPGSYGGETIYILGHCDGIICLVYHS---------GGLVFY
C8              LECRRKFHEPG-----STFGISCYCDGIICLADYG-------QKPNIVLC
C9              LLP-------------FSLEIAGHCDGIICLN-NS-------FLDDIVLC
C10             ICP-------------FSLQIAGHCDGLICLV-NI-------VNEEVALC
C11             KCS-------------LSLKIAGHCDGIICLV-NV---------EDVALC
C12             FEVL------------ESAWIIGHCHGIICLR-NA---------TKIILW
C13             ----------------ESLRIIGHCDGIVCLAL-IDYQQRLAKPSQVCLW
C14             VKTWA-----------EALIIIGHCNGIICLAQ--------AVSGEVIIC
                                    *   * *:. *               : : 

C1              NPAIKEFKILPN-QCL-------------------PNGTL---------N
C2              NPAIKEFKVIPE-PCLPRPRQFY------------FRCDA----------
C3              NPAIKEFKFLPE-SCL-------------------QDKNI---------G
C4              NPAIKEFKIILA-SCC-------------------HDCCW---------S
C5              NPAIKQFKILPK-PLL-------------------TNGIV---------N
C6              NPAMKEFKLLPK-SFLLLCNDDFDDLWS-------LSYELRYYT-----E
C7              NPSIREFKIIPP-SCL-------------------TESF----------S
C8              NPAIKEFKLLSE-SQLALSSPT-------------FRKT----------A
C9              NPATKESKLLPK-SCLLLPPRHPNDYDE-------IESDV---------N
C10             NPAIKEFKFLPR-SSLLLPRRHPEDDDG-------IESDV---------N
C11             NPSIKEFNHLPK-SCLLLPPKNWDDYENEDDYYEALESES---------N
C12             NPAIREVKV-TS-PYV-------------------PDENL---------S
C13             NPAIQQFKFLPEEPFLPDWSKVPHSRMVQEFAYLRPISLLNG-------E
C14             NPAIHEYKLLPPSPYL-------------------PDSDWPYSAIFRFRD
                **: :: :                                          

C1              SMA-FGYDPKSKDYKFLNIVDPSE-ETLGE----HRIVYDFP-RIEVYTL
C2              ----FGYDPKSEDYILVNVASYGE-NRYDD-----DRLVIEPLRAEMYTL
C3              SVG-FGYDPKSEDYILVSVVSYGHGEQYYN----DDRLVIDPMRAEVYTM
C4              TVG-FGYDLKCKDYIILEIACYGE-TNYND----PQRLVVDPPIAAVYTL
C5              SIG-FGYDARSKDYKVFSFPTHDE-DRSSE------RDFNYPPHVEVYSL
C6              QLG-FGYDPEGKDYKVLRFVIYDE-SCYWF-------------KAEVYTM
C7              CVGGFGYDPKCKDYKVVNIVPSGE-DSYDH----NQRLVIYPPRAEVYTL
C8              AVG-FGCDLMLKNYKVVRLINSGW--RYRD----DQDTVIPHLYAEVYNL
C9              AVG-FGYDSKAQEYKVVRIVS------FIT----G-VHKPLPSKAEVYTI
C10             AVG-FGYDSKTQDYKIVRVIT------YIT----G-IAYTLPSKAEVYTL
C11             AVG-FGYDSKANVYKVVRIVQ------FTS----GYVFTSHPSRVEVYTL
C12             DLG-IGYDPKSDTYKVVHISYGTQ-EEYGD----GHILIDRP-KTEVYTL
C13             TMG-FGYDPKSKDYKVIDIGFSDS-KFYGDPECYGGHVIVYPPKAVVYTL
C14             GLG-FGYDPNFNEYKIVNIGFPAP-ELSTP----DGYNIYNPPKAAVYTL
                    :* *   . * .. .                           :*.:

C1              STDSWREMKTYSLETETTMFLCFTK-----LYFNGFCYWIGCEKQKDFMD
C2              GTNSWREINIHNLETETTMFRPNHFQ----VYFKGNCYGLAEEIKKEFIS
C3              STDCWREIKIHNLETETTFFWPRHFQ----VYFKGNCYWLAHEKRKEFIT
C4              GIDSWREIKTDHLQTEDTYFWPTAFD----LYSKGIFYLFGYEEKKEFLD
C5              STDLWTEINADHLETETTNLYPEFFQ----MYFKGIWYWTGSEQQKEFMV
C6              DSNSWREIKTEYNNIIQFVNWSSDQP----IYFNGICYWQVSGSRGEF--
C7              STDSWRQIKIDYLETETTSFWPDIYQ----MCYKGVFYWLGHEQDKEYLC
C8              RTDSWKEIKIDGLLKENKIVVPDSNAQTKGLCSKGILYWCAMEEEKVLEV
C9              GTNSWREIKDQ-T--ESHVFWAASFK----LFLKGFYFWWA---------
C10             SSHSWREIKID-K--ECHVFWTPSFE----IHFRGIYYWSA---------
C11             GANCWREIKADVL--VSTVCWSPSFE----MYFKGIYYWDA---------
C12             GTDSWRQIMTGCLETETTHFWFQDFH----MYFNGFCYWNGREQLKEYQN
C13             QTDSWREIKTFSLERETSYLWPDTFQ----LYLKGVCYWLGYEQQKEFLC
C14             GTDAWRKIKTDTLETETTILWPQIFQ----MHFKDMCFWLAPEQHKE-LD
                  . * ::                      :  ..  :            

C1              YFDRDDEEW---VRQVIHSFDMSTEVFDHILLPNSLYLYEPLALYFNMHV
C2              SFDSLEEYY---IREVIVWFNTSDRVFHSALTPDCLY----RYPAHDFNL
C3              LYDRLEEYY---IWEAIVCFDTANRIFHNILVPDCLY----EFPMHDLDL
C4              DMERCEETN----KQVMILYDTRDELFHIAMLPDSFN--EPACGVHDIHV
C5              VYDSMDEEW---VRQLIIVFDMNDEVFEDILFPYSLY--GPMIPYLEMRV
C6              ----------------ILSFDMGNELFHEILNPDL----PDKCGVV--RL
C7              YYDRLSSPS---IRDVILLYDTGEEVFRTRLLPDSFK--DLGLHALSMSL
C8              TCDGDDEQKEIDMHACIISFNVGDESFHVINIGSY----DDHCCLIDGVL
C9              --SICPPEQ-----EIILSFDMNEELFHDIYIPESV---RHDIVRCNRGL
C10             -LTYPTPGA---DKEAIFAFDMSEETFEEIPIPDGICA-RDGIIKF---L
C11             -YSYLTPRQ---YKDGILAFDMSDELFYLIYHPETTR-------EFNKSL
C12             FYDLQEEHH---IRPVIISFDMGDEVFHNMLLPDFVY--ETYMWSYVLRL
C13             LFQTHQEEEE-RIARAIISFDTSDEVFHDIMLPHGLLEFYGFDNFLTLHL
C14             VLDEDEEQF---IREVIVMFDTGDELFHNIMLPDEFD--YPSKNYFVPNL
                                :  ::   . *                      :

C1              ILWNESIALFGLYHWRSooooooooo-oooooooo-oooooooooooooo
C2              TVWNNCVALFGYNRCGS--KPFEIWV-MGESDGFT-CSWIKHLSV--DIT
C3              AVWHDSIALFGFYRGGS--RPFEIWV-MDNFDGLN-SSWVKQLSV--DIA
C4              ALLNKSIALYGFSIFES-IHSIQIWV-TDDIRGAQEYSWTKYLSL-NPVD
C5              IVWNESVALFGQYRFGYADDAFGLWV-MDDI--VK-GSWTKQLTL-EVVV
C6              AVWKEFISLFTYQEEIVVPPSYDMWVMMDDLGDGK-GSWTKYFTI-GPVE
C7              TMWNGSIALFGFSYWGPDIESFKIWM-MDDF-----GSWTKHLTY-ETIM
C8              GLWKESIAL-CVRGW----TTLDIWV-MDDFGGGK-GSWTKYLAI-EPVV
C9              AVWKESIALLAY-GGDSGAQSFDIWV-IDDFGVFK-SSWIKYLTI-GPLE
C10             AVWKESVALISCIGDGP--KSFDIWV-MDDSSGIK-GSWTKHLVI-GPIE
C11             AVWKESIALITYEGDAP--KCFDLWL-NEDSSCFK-GLWTKYFTI-GPVE
C12             MAWNESVAIFGLDHGITSHESWGLWV-MDDFGGVT-GSWIKQFSFVSAVG
C13             TEWNESVALFSLLFEDE--HKATMWV-MDAK-----GAWTKQLTF-EYVD
C14             LVWKDSVALLGIQISQF--SSYGIWV-IDEFGGHNGGAWTKHITFELPVE
                   :  :::                                         

C1              oooooo-----ooooooo--ooooooo-----oooooooooooooooooo
C2              ESPQPL-----VLWESNQ--SLLVSPR-----IRVALYSFATKTFKYLPL
C3              KSPIPL-----ALWERNK--ILLVFTH-----TQIALYSFVTETYQYLPL
C4              NVRRSL-----AFWKIDE--VLMIAKD-----GRVVLCNLLTGKLKYFPI
C5              GTRMTL-----EMWKSDE--ILMVAND-----NRIFSYNIRTEEIKYLPI
C6              GDKWPL-----LFWKGDQ--LLMESND-----GQIVLYNIGTQILKYLPI
C7              GIYLSL-----VLWRSDD--VLMVAND-----GRIVSYSLSRDRVKYFPI
C8              KITSQFA----LFGKSDEQFVLVACDD-----SVVIFYDICTNKFNYLPL
C9              GISIPL-----IFWKSNE--FLMAATD-----GRLVSYNLSTQMFKYLPI
C10             -CEIPL-----VFWKSDE--LLLVISD-----GRVVSYHLGNKTIKYLPI
C11             -VEIPL-----VFWKSNE--ILMVNAD-----KHIVSYNLDTQTLKCLPM
C12             FLDTPL-----QIWKSDE--ILIVSKE-----RRVVSYNLDTEQYKYLPI
C13             YFPYSLPRKILAFWKSNE--IFGVGEN-----GSIVCYNLNTKIVKHLPI
C14             ----PL-----IFWKSDR--VLLNDPNDTDYRGLILDYNLDTKKLKNLPV
                                                                  

C1              ooooooooooooooo--ooooooooooooooooooooooooooooooooo
C2              CA---AEHFDAIPFV--NSIVPLNRDLVSVNISooooooooooooooooo
C3              YG---ASFFRL--FL--MWIVooooooooooooooooooooooooooooo
C4              HGLHLGDDIQGIVCV--DSIVPLNGRELSRHooooooooooooooooooo
C5              EST-HPTFSAAIVCI--NSIVPVIHGRQQAoooooooooooooooooooo
C6              HFIRDLYYSQELVYV--NSIVSINGGNVLEDIHISAFYGNGKFYSINKGD
C7              QG--VWGTYQAFVCVNSNSIVSVKGGNKVESRDIQTSNVLLooooooooo
C8              NGV-LLHHTQVVEYA--SSIVSVKECNKLDMEAooooooooooooooooo
C9              HGVEDPPYIQAVVYV--NSIVSVHASNKLEGINNSSoooooooooooooo
C10             HGVEDPQYIHAVVCV--NSMISVKKTKGoooooooooooooooooooooo
C11             HGVEDPEYIYAIIYV--SSIISVNRDNKLECTTTSIoooooooooooooo
C12             HSM-DSDYFEAVVYM--NSIVSVNGSKToooooooooooooooooooooo
C13             RS--VPDYF-------------------PPSRDTFYPFCCIAYVNSVVPI
C14             QS--ERSDSSAIVYV--SSIVSVLGGSKPKNKDNSTPNVooooooooooo
                                                                  

C1              ooooooooooooooooooooooooooooooooooo--
C2              ooooooooooooooooooooooooooooooooo----
C3              oooooooooooooooooooooooooooooooooo---
C4              ooooooooooooooooooooooooooooo--------
C5              ooooooooooooooooooooooooooooooooo----
C6              VIDISAFYGITSooooooooooooooooooooooo--
C7              oooooooooooooooooooooooooooooo-------
C8              oooooooooooooooooooooooooo-----------
C9              ooooooooooooooooooooooooooooooooo----
C10             ooooooooooooooooooooooooooooooooooo--
C11             oooooooooooooooooooooooooooo---------
C12             ooooooooooooooooooooooooooooooooooooo
C13             MNHVREHI-----------------------------
C14             oooooooooooooooooooo-----------------
                                                     




PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:09 - Revision 1613 - Build 432)
-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: 14 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  465 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: 14 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  465 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: 14 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  465 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: 14 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  465 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: 14 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  465 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: 14 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  465 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: 14 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  465 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: 14 SEQUENCES  [PROTEIN]
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C1  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C10 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C11 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C12 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C13 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C14 Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C2  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C3  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C4  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C5  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C6  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C7  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C8  Length  465 type PROTEIN Struct Unchecked
  Input File input.prot.fasta.muscle_rs_0_0.fasta.aln Seq C9  Length  465 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]: