--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Dec 09 17:18:08 WET 2016 codeml.models=0 1 2 3 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=CLUSTALW2 tcoffee.params= tcoffee.maxSeqs=0 codeml.bin=codeml mrbayes.tburnin=2500 codeml.dir= input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb_adops tcoffee.bin=t_coffee_ADOPS mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta=/opt/ADOPS/442/Zasp52-PT/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/442/Zasp52-PT/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/442/Zasp52-PT/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Use the harmonic mean for Bayes factor comparisons of models) (Values are saved to the file /opt/ADOPS/442/Zasp52-PT/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -4895.77 -4909.85 2 -4896.10 -4909.80 -------------------------------------- TOTAL -4895.92 -4909.83 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/442/Zasp52-PT/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/442/Zasp52-PT/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": Summaries are based on a total of 3002 samples from 2 runs. Each run produced 2001 samples of which 1501 samples were included. Parameter summaries saved to file "/opt/ADOPS/442/Zasp52-PT/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 0.416783 0.001308 0.349681 0.490179 0.414564 1470.12 1485.56 1.001 r(A<->C){all} 0.058600 0.000163 0.033549 0.082300 0.057868 1023.68 1035.66 1.001 r(A<->G){all} 0.230625 0.000909 0.171425 0.288073 0.229539 673.95 817.79 1.000 r(A<->T){all} 0.120952 0.000627 0.073405 0.170527 0.119928 692.93 868.06 1.000 r(C<->G){all} 0.051913 0.000120 0.032593 0.074835 0.051393 1139.62 1158.56 1.000 r(C<->T){all} 0.423088 0.001310 0.357343 0.496595 0.423208 733.93 751.52 1.000 r(G<->T){all} 0.114821 0.000542 0.071880 0.161895 0.113363 1121.16 1121.60 1.000 pi(A){all} 0.238761 0.000084 0.219834 0.255583 0.238548 1237.38 1242.48 1.000 pi(C){all} 0.334459 0.000096 0.315871 0.353390 0.334256 1249.56 1324.01 1.000 pi(G){all} 0.262881 0.000093 0.245176 0.282294 0.262763 1065.84 1157.62 1.000 pi(T){all} 0.163899 0.000059 0.148681 0.178454 0.163720 1080.57 1117.40 1.000 alpha{1,2} 0.116269 0.000379 0.077889 0.153112 0.115274 1117.29 1228.23 1.000 alpha{3} 2.939687 0.749378 1.413131 4.623084 2.831726 1277.17 1318.07 1.000 pinvar{all} 0.607501 0.001029 0.546485 0.669720 0.609270 1333.65 1366.36 1.001 ------------------------------------------------------------------------------------------------------ * 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 -4320.026444 Model 2: PositiveSelection -4320.026445 Model 0: one-ratio -4356.676505 Model 3: discrete -4318.484855 Model 7: beta -4320.11154 Model 8: beta&w>1 -4319.08469 Model 0 vs 1 73.30012200000056 Model 2 vs 1 2.0000006770715117E-6 Model 8 vs 7 2.05370000000039
>C1 MAQPQLLQIKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS EVLKFLREEETGQSTPAFGNSHYEHDAPQQLQQPQQQYNQHQQHYHQQQQ QQQSSTTRHVSAPVNSPKPPSTGGLPTGQNICTECERLITGVFVRIKDKN LHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAKQAAINNPPTGTEGYVP VPIKPNTKLSASTISSALNSHGYGGHSNGYSNGNSTPAPAPVNQGYARPF GAAAPKSPVSYPPQQQQQSPRPAPGGQNPYATLPRSNVGQQGAGGKSAGA FGATSAPKRGRGILNKAAGPGVRIPLCNSCNVQIRGPFITALGRIWCPDH FICVNGNCRRPLQDIGFVEEKGDLYCEYCFEKYLAPTCSKCAGKIKGDCL NAIGKHFHPECFTCGQCGKIFGNRPFFLEDGNAYCEADWNELFTTKCFAC GFPVEAGDRWVEALNHNYHSQCFNCTFCKQNLEGQSFYNKGGRPFCKNHA Rooooooooooooooo >C2 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS EVLKFLRVEETGQSTPAFGNSHYEHDAPQQVQQQQQPQQQYNQHQQHYHQ QQQQQQSSTTRHVSAPVNSPKPPSTGGLPTGQNICTECERLITGVFVRIK DKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAKQAAINNPPTGTEG YVPVPIKPNTKLSASTISSALNSHGYGGNSNGYSNGNSTPAPAPVNQGYA RPFGAAAPKSPVSYPPQQQQQSPRPAPGGQNPYATLPRSNVGQQGAGGKS AGAFGATSAPKRGRGILNKAAGPGVRIPLCNSCNVQIRGPFITALGRIWC PDHFICVNGNCRRPLQDIGFVEEKGDLYCEYCFEKYLAPTCSKCAGKIKG DCLNAIGKHFHPECFTCGQCGKVFGNRPFFLEDGNAYCEADWNELFTTKC FACGFPVEAGDRWVEALNHNYHSQCFNCTFCKQNLEGQSFYNKGGRPFCK NHARoooooooooooo >C3 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS EVLKFLREEETGQSTPAFGNSHYEHDAPQQLQQQQQPQQQYNQHQQHYHQ QQQQQQSSTTRHVSAPVNSPKPPSTGGLPTGQNICTECERLITGVFVRIK DKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAKQAAINNPPTGTEG YVPVPIKPNTKLSASTISSALNSHGYGGNSNGYSNGNSTPAPAPVNQGYA RPFGAAAPKSPVSYPPQQQQQSPRPAPGGQNPYATLPRSNVGQQGAGGKS AGAFGATSAPKRGRGILNKAAGPGVRIPLCNSCNVQIRGPFITALGRIWC PDHFICVNGNCRRPLQDIGFVEEKGDLYCEYCFEKYLAPTCSKCAGKIKG DCLNAIGKHFHPECFTCGQCGKIFGNRPFFLEDGNAYCEADWNELFTTKC FACGFPVEAGDRWVEALNHNYHSQCFNCTFCKQNLEGQSFYNKGGRPFCK NHARoooooooooooo >C4 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFANGGDGGVKS IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS EVLKFLREEETGQSTPAFGNSHYEHDAPQQQQQQYQQPQQQYNQHQQHYH QQQQQQQQQQSSATRHVSAPVNSPKPPSTGGLPTGQNICTECERLITGVF VRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAKQAAINNPPT GTEGYVPVPIKPNTKLSASTISSALNSHGYGGNSNGYSNGNSTPAPAPVN QGYARPFGAAAPKSPVSYPPQQQQQSPRPGGQNPYATLPRSNVGQQGAGG KSAGAFGATSAPKRGRGILNKAAGPGVRIPLCNSCNVQIRGPFITALGRI WCPDHFICVNGNCRRPLQDIGFVEEKGDLYCEYCFEKYLAPTCSKCAGKI KGDCLNAIGKHFHPECFTCGQCGKIFGNRPFFLEDGNAYCEADWNELFTT KCFACGFPVEAGDRWVEALNHNYHSQCFNCTFCKQNLEGQSFYNKGGRPF CKNHARoooooooooo >C5 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS EVLKFLREEETGQSTPAFGNSHYEHDAPQQLQQQQQQQQPQQQYNQHQHQ QHYHQQQQQQSSTTRHVSAPVNSPKPPSTGGLPTGQNICTECERLITGVF VRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAKQAAINNPPS GTEGYVPVPIKPNTKLSASTISSALNSHGYGGSSNGYSNGNSAPAPAPVN QGYARPFGAAAPKSPVSYPPQQQQQQSPRPAPGGQNPYATLPRSNVGQQG AGGKSAGAFGATSAPKRGRGILNKAAGPGVRIPLCNSCNVQIRGPFITAL GRIWCPDHFICVNGNCRRPLQDIGFVEEKGDLYCEYCFEKYLAPTCSKCA GKIKGDCLNAIGKHFHPECFTCGQCGKIFGNRPFFLEDGNAYCEADWNEL FTTKCFACGFPVEAGDRWVEALNHNYHSQCFNCTFCKQNLEGQSFYNKGG RPFCKNHARooooooo >C6 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFANGGDGGVKS IVNKQYNTPVGIYSEESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS EVLKFLREEESGQSTPAFGNSHYEHDAPRQQQQPQQQYNQQQQHYHQQQQ QQQSSATRHVSAPVNSPKPPSTGGLPTGQNICTECERLITGVFVRIKDKN LHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAKQAAINNPPSGTEGYVP VPIKPNTKLSASTISSALNSHGYGGNSNGYSNGNSAPAPAPVNQGYARPF GAAAPKSPVSYPVQQQQQSPRPAPGGNNPYATLPRSNVGQQGAGGKSAGA FGATSAPKRGRGILNKAAGPGVRIPLCNSCNVQIRGPFITALGRIWCPDH FICVNGNCRRPLQDIGFVEEKGDLYCEYCFEKYLAPTCSKCAGKIKGDCL NAIGKHFHPECFTCGQCGKIFGNRPFFLEDGNAYCEADWNELFTTKCFAC GFPVEAGDRWVEALNHNYHSQCFNCTFCKQNLEGQSFYNKGGRPFCKNHA Rooooooooooooooo >C7 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFANGGDGGVKS IVNKQYNTPVGIYSEESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS EVLKFLREEETGQSTPAFGNSHCEHDAPRQQQQQQPQQQQQYNQQQQHYH QQQQQQQQQSSTTRHVSAPVNSPKPPSTGGLPTGQNICTECERLITGVFV RIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHARQAAINNPPTG TEGYVPVPIKPNTKLSASTISSALNTHGYGGNSNGYSNGNSAPAPAPVNQ GYARPFGAAAPKSPVSYPVQQQQQQSPRPAPGGNNPYATLPRSNVGQQGA GAGGKSAGAFGATSAPKRGRGILNKAAGPGVRIPLCNSCNVQIRGPFITA LGRIWCPDHFICVNGNCRRPLQDIGFVEEKGDLYCEYCFEKYLAPTCSKC AGKIKGDCLNAIGKHFHPECFTCGQCGKIFGNRPFFLEDGNAYCEADWNE LFTTKCFACGFPVEAGDRWVEALNHNYHSQCFNCTFCKQNLEGQSFYNKG GRPFCKNHARoooooo >C8 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS EVLKFLREEETGQSTPAFGNSHYEHDAPHQQQQQQQQQYNHQQQYNQQQH YHQQQQHQQQQQSSTTRHVSAPVNSPKPPSTGGLPTGQNICTECERLITG VFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAKQAAINNP PSGTEGYVPVPIKPNTKLSASTISSALNSHGYGGSSNGYSNGNSTPAPAK VNQGYARPFGAAAPKSPVSYPPQQQQQSPRPAPGNNNINNNPYATLPRSN VGQQGAGNKSAGAFGATSAPKRGRGILNKAAGPGVRIPLCNSCNVQIRGP FITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGDLYCEYCFEKYLAPT CSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKIFGNRPFFLEDGNAYCEA DWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCFNCTFCKQNLEGQSF YNKGGRPFCKNHARoo >C9 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS EVLKFLREEETGQSTPAFGNSHYEHDAPQQQQQQQQPQQQYNQHQQHHQQ QQQLQQQSSTTRHVSAPVNSPKPPSTGGLPTGQNICTECERLITGVFVRI KDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAKQAAINNPPSGTE GYVPVPIKPNTKLSATTISSALNSHGYGGSNSNGYSNGNSAPAPAPVNQG YARPFGAAAPKSPVSYPPQQQQQSPRPAPGGNINNNNPYATLPRSNVGQQ GAGNKGAGAFGATSAPKRGRGILNKAAGPGVRIPLCNSCNVQIRGPFITA LGRIWCPDHFICVNGNCRRPLQDIGFVEEKGDLYCEYCFEKYLAPTCSKC AGKIKGDCLNAIGKHFHPECFTCGQCGKIFGNRPFFLEDGNAYCEADWNE LFTTKCFACGFPVEAGDRWVEALNHNYHSQCFNCTFCKQNLEGQSFYNKG GRPFCKNHARoooooo >C10 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS EVLKFLREEETGQSTPAFGNSHYEHDAPQQQQQPQQQQYNQQQHQQQHYH QQHHQQQQQQQLSSTTRHVSAPVNSPKPPSTGGLPTGQNICTECERLITG VFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAKQAAINNP PSGTEGYVPVPIKPNTKLSASTISTALNSHGYGGSNSNGYSNGNSAPAPV NQGYARPFGAAAPKSPVASYPPQQQQQSPRPAPGGNNNFNNNNAYATLPR SNVGQQGAGNKSAGAFGATSAPKRGRGILNKAAGPGVRIPLCNSCNVQIR GPFITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGDLYCEYCFEKYLA PTCSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKIFGNRPFFLEDGNAYC EADWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCFNCTFCKQNLEGQ SFYNKGGRPFCKNHAR CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE: ], CPU=0.00 sec, SCORE=100, Nseq=10, Len=693 C1 MAQPQLLQIKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ C2 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ C3 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ C4 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ C5 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ C6 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ C7 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ C8 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ C9 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ C10 MAQPQLLQVKLSRFDAQPWGFRLQGGTDFAQPLLVQKVNAGSLSEQAGLQ ********:***************************************** C1 PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT C2 PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT C3 PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT C4 PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT C5 PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT C6 PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT C7 PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT C8 PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT C9 PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT C10 PGDAVVKINDVDVFNLRHKDAQDIVVRSGNNFVITVQRGGSTWRPHVTPT ************************************************** C1 GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS C2 GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS C3 GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS C4 GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFANGGDGGVKS C5 GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS C6 GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFANGGDGGVKS C7 GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFANGGDGGVKS C8 GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS C9 GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS C10 GNVPQPNSPYLQTVTKTSLAHKQQDSQHIGCGYNNAARPFSNGGDGGVKS ****************************************:********* C1 IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS C2 IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS C3 IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS C4 IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS C5 IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS C6 IVNKQYNTPVGIYSEESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS C7 IVNKQYNTPVGIYSEESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS C8 IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS C9 IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS C10 IVNKQYNTPVGIYSDESIAETLSAQAEVLAGGVLGVNFKKNEKEYQGDRS **************:*********************************** C1 EVLKFLREEETGQSTPAFGNSHYEHDAPQQLQQP------QQQYNQHQ-- C2 EVLKFLRVEETGQSTPAFGNSHYEHDAPQQVQQQ---QQPQQQYNQHQ-- C3 EVLKFLREEETGQSTPAFGNSHYEHDAPQQLQQQ---QQPQQQYNQHQ-- C4 EVLKFLREEETGQSTPAFGNSHYEHDAPQQQQQQY--QQPQQQYNQHQ-- C5 EVLKFLREEETGQSTPAFGNSHYEHDAPQQLQQQQQQQQPQQQYNQHQH- C6 EVLKFLREEESGQSTPAFGNSHYEHDAPRQQQQPQ------QQYNQQQ-- C7 EVLKFLREEETGQSTPAFGNSHCEHDAPRQQQQQQ--PQQQQQYNQQQ-- C8 EVLKFLREEETGQSTPAFGNSHYEHDAPHQQQQQQ-----QQQYNHQQQY C9 EVLKFLREEETGQSTPAFGNSHYEHDAPQQQQQQQ---QPQQQYNQHQ-- C10 EVLKFLREEETGQSTPAFGNSHYEHDAPQQQQQPQ-----QQQYNQQQ-- ******* **:*********** *****:* ** ****::* C1 ---QHYHQQ--QQQQ---QSSTTRHVSAPVNSPKPPSTGGLPTGQNICTE C2 ---QHYHQQ--QQQQ---QSSTTRHVSAPVNSPKPPSTGGLPTGQNICTE C3 ---QHYHQQ--QQQQ---QSSTTRHVSAPVNSPKPPSTGGLPTGQNICTE C4 ---QHYHQQ--QQQQQQQQSSATRHVSAPVNSPKPPSTGGLPTGQNICTE C5 --QQHYHQQ--QQQQ----SSTTRHVSAPVNSPKPPSTGGLPTGQNICTE C6 ---QHYHQQ--QQQQQ---SSATRHVSAPVNSPKPPSTGGLPTGQNICTE C7 ---QHYHQQ--QQQQQQ-QSSTTRHVSAPVNSPKPPSTGGLPTGQNICTE C8 NQQQHYHQQQQHQQQQQ--SSTTRHVSAPVNSPKPPSTGGLPTGQNICTE C9 ---QHHQQQ--QQLQQ--QSSTTRHVSAPVNSPKPPSTGGLPTGQNICTE C10 HQQQHYHQQHHQQQQQQQLSSTTRHVSAPVNSPKPPSTGGLPTGQNICTE **::** :* * **:**************************** C1 CERLITGVFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAK C2 CERLITGVFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAK C3 CERLITGVFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAK C4 CERLITGVFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAK C5 CERLITGVFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAK C6 CERLITGVFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAK C7 CERLITGVFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAR C8 CERLITGVFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAK C9 CERLITGVFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAK C10 CERLITGVFVRIKDKNLHVECFKCATCGTSLKNQGYYNFNNKLYCDIHAK *************************************************: C1 QAAINNPPTGTEGYVPVPIKPNTKLSASTISSALNSHGYGG-HSNGYSNG C2 QAAINNPPTGTEGYVPVPIKPNTKLSASTISSALNSHGYGG-NSNGYSNG C3 QAAINNPPTGTEGYVPVPIKPNTKLSASTISSALNSHGYGG-NSNGYSNG C4 QAAINNPPTGTEGYVPVPIKPNTKLSASTISSALNSHGYGG-NSNGYSNG C5 QAAINNPPSGTEGYVPVPIKPNTKLSASTISSALNSHGYGG-SSNGYSNG C6 QAAINNPPSGTEGYVPVPIKPNTKLSASTISSALNSHGYGG-NSNGYSNG C7 QAAINNPPTGTEGYVPVPIKPNTKLSASTISSALNTHGYGG-NSNGYSNG C8 QAAINNPPSGTEGYVPVPIKPNTKLSASTISSALNSHGYGGS-SNGYSNG C9 QAAINNPPSGTEGYVPVPIKPNTKLSATTISSALNSHGYGGSNSNGYSNG C10 QAAINNPPSGTEGYVPVPIKPNTKLSASTISTALNSHGYGGSNSNGYSNG ********:******************:***:***:***** ******* C1 NSTPAPAPVNQGYARPFGAAAPKSPVS-YPPQQQQQ-SPRPAPGG----- C2 NSTPAPAPVNQGYARPFGAAAPKSPVS-YPPQQQQQ-SPRPAPGG----- C3 NSTPAPAPVNQGYARPFGAAAPKSPVS-YPPQQQQQ-SPRPAPGG----- C4 NSTPAPAPVNQGYARPFGAAAPKSPVS-YPPQQQQQ-SPR--PGG----- C5 NSAPAPAPVNQGYARPFGAAAPKSPVS-YPPQQQQQQSPRPAPGG----- C6 NSAPAPAPVNQGYARPFGAAAPKSPVS-YPVQQQQQ-SPRPAPGG----- C7 NSAPAPAPVNQGYARPFGAAAPKSPVS-YPVQQQQQQSPRPAPGG----- C8 NSTPAPAKVNQGYARPFGAAAPKSPVS-YPPQQQQQ-SPRPAPGNNN--I C9 NSAPAPAPVNQGYARPFGAAAPKSPVS-YPPQQQQQ-SPRPAPGGNI--N C10 NSAPAP--VNQGYARPFGAAAPKSPVASYPPQQQQQ-SPRPAPGGNNNFN **:*** ******************: ** ***** *** **. C1 -QNPYATLPRSNVGQQ--GAGGKSAGAFGATSAPKRGRGILNKAAGPGVR C2 -QNPYATLPRSNVGQQ--GAGGKSAGAFGATSAPKRGRGILNKAAGPGVR C3 -QNPYATLPRSNVGQQ--GAGGKSAGAFGATSAPKRGRGILNKAAGPGVR C4 -QNPYATLPRSNVGQQ--GAGGKSAGAFGATSAPKRGRGILNKAAGPGVR C5 -QNPYATLPRSNVGQQ--GAGGKSAGAFGATSAPKRGRGILNKAAGPGVR C6 -NNPYATLPRSNVGQQ--GAGGKSAGAFGATSAPKRGRGILNKAAGPGVR C7 -NNPYATLPRSNVGQQGAGAGGKSAGAFGATSAPKRGRGILNKAAGPGVR C8 NNNPYATLPRSNVGQQ--GAGNKSAGAFGATSAPKRGRGILNKAAGPGVR C9 NNNPYATLPRSNVGQQ--GAGNKGAGAFGATSAPKRGRGILNKAAGPGVR C10 NNNAYATLPRSNVGQQ--GAGNKSAGAFGATSAPKRGRGILNKAAGPGVR :*.************ ***.*.************************** C1 IPLCNSCNVQIRGPFITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGD C2 IPLCNSCNVQIRGPFITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGD C3 IPLCNSCNVQIRGPFITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGD C4 IPLCNSCNVQIRGPFITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGD C5 IPLCNSCNVQIRGPFITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGD C6 IPLCNSCNVQIRGPFITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGD C7 IPLCNSCNVQIRGPFITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGD C8 IPLCNSCNVQIRGPFITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGD C9 IPLCNSCNVQIRGPFITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGD C10 IPLCNSCNVQIRGPFITALGRIWCPDHFICVNGNCRRPLQDIGFVEEKGD ************************************************** C1 LYCEYCFEKYLAPTCSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKIFGN C2 LYCEYCFEKYLAPTCSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKVFGN C3 LYCEYCFEKYLAPTCSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKIFGN C4 LYCEYCFEKYLAPTCSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKIFGN C5 LYCEYCFEKYLAPTCSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKIFGN C6 LYCEYCFEKYLAPTCSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKIFGN C7 LYCEYCFEKYLAPTCSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKIFGN C8 LYCEYCFEKYLAPTCSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKIFGN C9 LYCEYCFEKYLAPTCSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKIFGN C10 LYCEYCFEKYLAPTCSKCAGKIKGDCLNAIGKHFHPECFTCGQCGKIFGN **********************************************:*** C1 RPFFLEDGNAYCEADWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCF C2 RPFFLEDGNAYCEADWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCF C3 RPFFLEDGNAYCEADWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCF C4 RPFFLEDGNAYCEADWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCF C5 RPFFLEDGNAYCEADWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCF C6 RPFFLEDGNAYCEADWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCF C7 RPFFLEDGNAYCEADWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCF C8 RPFFLEDGNAYCEADWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCF C9 RPFFLEDGNAYCEADWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCF C10 RPFFLEDGNAYCEADWNELFTTKCFACGFPVEAGDRWVEALNHNYHSQCF ************************************************** C1 NCTFCKQNLEGQSFYNKGGRPFCKNHARooooooooooooooo C2 NCTFCKQNLEGQSFYNKGGRPFCKNHARoooooooooooo--- C3 NCTFCKQNLEGQSFYNKGGRPFCKNHARoooooooooooo--- C4 NCTFCKQNLEGQSFYNKGGRPFCKNHARoooooooooo----- C5 NCTFCKQNLEGQSFYNKGGRPFCKNHARooooooo-------- C6 NCTFCKQNLEGQSFYNKGGRPFCKNHARooooooooooooooo C7 NCTFCKQNLEGQSFYNKGGRPFCKNHARoooooo--------- C8 NCTFCKQNLEGQSFYNKGGRPFCKNHARoo------------- C9 NCTFCKQNLEGQSFYNKGGRPFCKNHARoooooo--------- C10 NCTFCKQNLEGQSFYNKGGRPFCKNHAR--------------- **************************** PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:04 - Revision 1613 - Build 427) -full_log S [0] -genepred_score S [0] nsd -run_name S [0] -mem_mode S [0] mem -extend D [1] 1 -extend_mode S [0] very_fast_triplet -max_n_pair D [0] 10 -seq_name_for_quadruplet S [0] all -compact S [0] default -clean S [0] no -do_self FL [0] 0 -do_normalise D [0] 1000 -template_file S [0] -setenv S [0] 0 -template_mode S [0] -flip D [0] 0 -remove_template_file D [0] 0 -profile_template_file S [0] -in S [0] -seq S [0] -aln S [0] -method_limits S [0] -method S [0] -lib S [0] -profile S [0] -profile1 S [0] -profile2 S [0] -pdb S [0] -relax_lib D [0] 1 -filter_lib D [0] 0 -shrink_lib D [0] 0 -out_lib W_F [0] no -out_lib_mode S [0] primary -lib_only D [0] 0 -outseqweight W_F [0] no -dpa FL [0] 0 -seq_source S [0] ANY -cosmetic_penalty D [0] 0 -gapopen D [0] 0 -gapext D [0] 0 -fgapopen D [0] 0 -fgapext D [0] 0 -nomatch D [0] 0 -newtree W_F [0] default -tree W_F [0] NO -usetree R_F [0] -tree_mode S [0] nj -distance_matrix_mode S [0] ktup -distance_matrix_sim_mode S [0] idmat_sim1 -quicktree FL [0] 0 -outfile W_F [0] default -maximise FL [1] 1 -output S [1] score_ascii html score_ascii -len D [0] 0 -infile R_F [1] /opt/ADOPS/442/Zasp52-PT/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln -matrix S [0] default -tg_mode D [0] 1 -profile_mode S [0] cw_profile_profile -profile_comparison S [0] profile -dp_mode S [0] linked_pair_wise -ktuple D [0] 1 -ndiag D [0] 0 -diag_threshold D [0] 0 -diag_mode D [0] 0 -sim_matrix S [0] vasiliky -transform S [0] -extend_seq FL [0] 0 -outorder S [0] input -inorder S [0] aligned -seqnos S [0] off -case S [0] keep -cpu D [0] 0 -maxnseq D [0] 1000 -maxlen D [0] -1 -sample_dp D [0] 0 -weight S [0] default -seq_weight S [0] no -align FL [1] 1 -mocca FL [0] 0 -domain FL [0] 0 -start D [0] 0 -len D [0] 0 -scale D [0] 0 -mocca_interactive FL [0] 0 -method_evaluate_mode S [0] default -evaluate_mode S [1] t_coffee_fast -get_type FL [0] 0 -clean_aln D [0] 0 -clean_threshold D [1] 1 -clean_iteration D [1] 1 -clean_evaluate_mode S [0] t_coffee_fast -extend_matrix FL [0] 0 -prot_min_sim D [40] 40 -prot_max_sim D [90] 90 -prot_min_cov D [40] 40 -pdb_type S [0] d -pdb_min_sim D [35] 35 -pdb_max_sim D [100] 100 -pdb_min_cov D [50] 50 -pdb_blast_server W_F [0] EBI -blast W_F [0] -blast_server W_F [0] EBI -pdb_db W_F [0] pdb -protein_db W_F [0] uniprot -method_log W_F [0] no -struc_to_use S [0] -cache W_F [0] use -align_pdb_param_file W_F [0] no -align_pdb_hasch_mode W_F [0] hasch_ca_trace_bubble -external_aligner S [0] NO -msa_mode S [0] tree -master S [0] no -blast_nseq D [0] 0 -lalign_n_top D [0] 10 -iterate D [1] 0 -trim D [0] 0 -split D [0] 0 -trimfile S [0] default -split D [0] 0 -split_nseq_thres D [0] 0 -split_score_thres D [0] 0 -check_pdb_status D [0] 0 -clean_seq_name D [0] 0 -seq_to_keep S [0] -dpa_master_aln S [0] -dpa_maxnseq D [0] 0 -dpa_min_score1 D [0] -dpa_min_score2 D [0] -dpa_keep_tmpfile FL [0] 0 -dpa_debug D [0] 0 -multi_core S [0] templates_jobs_relax_msa_evaluate -n_core D [0] 0 -max_n_proc D [0] 0 -lib_list S [0] -prune_lib_mode S [0] 5 -tip S [0] none -rna_lib S [0] -no_warning D [0] 0 -run_local_script D [0] 0 -plugins S [0] default -proxy S [0] unset -email S [0] -clean_overaln D [0] 0 -overaln_param S [0] -overaln_mode S [0] -overaln_model S [0] -overaln_threshold D [0] 0 -overaln_target D [0] 0 -overaln_P1 D [0] 0 -overaln_P2 D [0] 0 -overaln_P3 D [0] 0 -overaln_P4 D [0] 0 -exon_boundaries S [0] -dump S [0] no -display D [0] 100 INPUT FILES Input File (S) /opt/ADOPS/442/Zasp52-PT/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 10 SEQUENCES [PROTEIN] Input File /opt/ADOPS/442/Zasp52-PT/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length 666 type PROTEIN Struct Unchecked Input File /opt/ADOPS/442/Zasp52-PT/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length 666 type PROTEIN Struct Unchecked Input File /opt/ADOPS/442/Zasp52-PT/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length 666 type PROTEIN Struct Unchecked Input File /opt/ADOPS/442/Zasp52