--- 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