--- 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