--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Nov 22 06:17:04 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/3/Acox57D-d-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/Acox57D-d-PA/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/3/Acox57D-d-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -7557.72         -7575.42
2      -7557.41         -7574.25
--------------------------------------
TOTAL    -7557.55         -7575.00
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/Acox57D-d-PA/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/3/Acox57D-d-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.161153    0.004077    1.044392    1.289412    1.160457   1370.79   1429.10    1.000
r(A<->C){all}   0.092686    0.000153    0.068154    0.116543    0.092092   1011.54   1018.22    1.000
r(A<->G){all}   0.249881    0.000408    0.209981    0.289022    0.249353    980.53    980.94    1.002
r(A<->T){all}   0.143455    0.000294    0.109770    0.175950    0.143231    696.19    886.95    1.000
r(C<->G){all}   0.065578    0.000074    0.048966    0.082282    0.065385    984.64    994.76    1.000
r(C<->T){all}   0.377555    0.000548    0.335084    0.426403    0.376950    794.53    825.82    1.000
r(G<->T){all}   0.070844    0.000118    0.050676    0.092927    0.070315    962.16   1053.19    1.000
pi(A){all}      0.241702    0.000084    0.223741    0.260048    0.241596   1043.92   1069.90    1.000
pi(C){all}      0.277903    0.000080    0.260261    0.294959    0.277783   1026.67   1176.46    1.000
pi(G){all}      0.272576    0.000083    0.253790    0.289398    0.272460   1132.46   1182.31    1.000
pi(T){all}      0.207819    0.000062    0.192696    0.223192    0.207696   1061.23   1135.48    1.000
alpha{1,2}      0.140769    0.000112    0.118947    0.161177    0.140116   1397.63   1424.56    1.001
alpha{3}        4.931885    1.217613    2.885863    7.106033    4.794416   1244.89   1321.26    1.000
pinvar{all}     0.316835    0.000854    0.260990    0.372504    0.317535   1065.57   1283.28    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	-7141.891516
Model 2: PositiveSelection	-7141.891517
Model 0: one-ratio	-7187.912203
Model 3: discrete	-7121.540049
Model 7: beta	-7121.740835
Model 8: beta&w>1	-7121.722865


Model 0 vs 1	92.04137400000036

Model 2 vs 1	2.0000006770715117E-6

Model 8 vs 7	0.035939999999754946
>C1
MSHIKNLIPSTVNPDLQKERAAAEFHVEEFSAWWHGGQDKLKKKREIEKA
IFSDLEDGYGLNHEYMSHEEVYNSTVKKVAEAAVKLKALQNKLNPGGTDI
WPGGLFNAQSFGLFPANHPIATHITMFVDVIKGQGTAEQVEKWGKAAENC
NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
GHTANHAMVVAQLYIADVHHGVQMFIVPLRDSETHMPLPGVDIGEIGKKL
GMASVNQGFLGLNHVRIPRTNMLMKFAKVERDGTFKASPASRINYLTMVY
TRCLIVSQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
LFPEIATGIAYHLATEYMWEMYAQTVQEANNGKFERLPDMHILSCALKVL
CTTDGCAGIEKLRLSTGGHGYLIAANLSNIYGNAVAAYTYEGENTVLLLQ
IGRALVKAWASFVDKKPLSASYSYFASSMQLKEFPKWDDSWQCIIKALQY
TAAHKTRIAFENLANRMASGQSQGVAANNTGIELTRAAELHGRQFVCQTF
LEQITGAKAQKRSPALNKILENVLELFLVQTVLNNLNDILRFIKLSDADL
RSLQKRLEDSLAQFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
AKRSTMNQKPVQTSFETYLKPLMKAKL
>C2
MSHIKNLIPSTVNPFLQKERAEAEFNVEEFSAWWHGGQDKLKKKREIEKA
IFSDLEDGYGLNHEYMSHEEVYNSTVKKVAEASVKLKALQNKLNPGGTDI
WPGGLFNAQSFGLFPANHPVATHITMFVDVIKGQGTAEQVEKWGKPAENC
NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
GHTANHAMVVAQLYIADVHHGVQMFIVPVRDSETHMALPGVDIGEIGKKL
GMASVNQGFLGLNHVRIPRTNMLMKFAKVERDGTFKASPASRINYLTMVY
TRCLIVSQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
LFPEIATGIAYHLATEYVWEMYAQTVQEANNGKFERLPDMHILSCALKVL
CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAYTYEGENTVLLLQ
IGRALVKAWASFVDKKPLSASYSYFASSMQLKEFPKWDDSWQCIIKALQY
TAAHKTRIAFENLANRMASGQSQGVAANNTGIELTRAAELHGRQFVCQTF
LEQITGAKAQKRSPALNKILENVLELFLVQTVLNNLNDILRFIKLSDADL
RSLQKRLEDSLEQFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
AKRSTMNQKPVQTSFESYLKPLMKAKL
>C3
MSHIKNLIPSTVNPDLQKERSAAEFNVEEFSAWWHGGQDKLKKKREIEKA
IFSDLEDGYGLNHEYMSHEEVYNSTVKKVAEAAVKLKALQNKLNPGGTDI
WPGGLFNAQSFGLFPANHPVATHITMFVDVIKGQGTAEQVEKWGKAAENC
NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
GHTANHAMVVAQLYIADVHHGVQMFIVPVRDSETHMPLPGVDIGEIGKKL
GMASVNQGFLGLNHVRIPRTNMLMKFAKVERDGTFKASPASRINYLTMVY
TRCLIVSQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
LFPEIATGIAYHLATEYVWEMYAQTVQEANNGKFERLPDMHILSCALKVL
CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAYTYEGENTVLLLQ
IGRALVKAWASFVDKKPLSASYSYFASSMQLKEFPKWDDSWQCIIKALQY
TAAHKTRIAFENLANRMASGQSQGVAANNTGIELTRAAELHGRQFVCQTF
LEQITGAKAQKRSPALNKILENVLELFLVQTVLNNLNDILRFIQLSDADL
RSLQRRLEDSLEQFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
AKRSTMNQKPVQTSFETYLKPLMKAKL
>C4
MSHIKNLIPSTVNPDLQKERTGAEFDVEEFSAWWHGGQDKLKRKREIEEA
IFSDLEDGYGLNHEYMSHEEVYNSTVKKVAEAAVKLKALQNKLNPGGTDI
WPGGLYNAQSYGLFPANHPVATHITMFVDVIKGQGTAEQAEKWGKAAANC
NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
GHTANHAMVVAQLYIADVHHGVQMFIVPLRDSETHMPLPGVDIGEVGKKL
GMASVNQGFLGLDHVRIPRTNMLMKFAKVERDGTFKASPASRINYLTMVY
TRCLIVSQNSMLHLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
LFPEIATGIAYHLATEYVWEMYDQTVLEANNGKFERLPDMHILSCALKVL
CTTDGCAGIERLRLSTGGHGYLIAANLSNIYGNAVAAYTYEGENTVLLLQ
IGRALVKAWASFVEQKPLSASYSYFATSMQLKEFPKWDDSWQCIIKALQY
TAAHKTRIAFENLANRMASGQSQGAAANNTGIELTRAAELHGRQFVCQTF
LEQITGAKAQKRSPALNRILENVLELFLVQTVLNNLNDILRFINLSDADL
RSLQKRLEDALERFRPNAVAICDGFGFHDRVLNSVLGSYDGNVYPRLFDS
AKRSTMNQKPVQTSFETHLKPLMKAKL
>C5
MSHIKNLIPSTVNPDLQKERTGAEFNVEEFSAWWHGGQDKLKKKREIEKA
LFSDLEDGYGLNHEYMSHEEVYNSSVKKVAEAAVKLKALQNKLNPGGTDI
WPGGLFNAQSFGLFPANHPVATHITMFVDVIKGQGTPEQVEKWGKAAENC
NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
GHTANHAMVVAQLYIADVHHGVQMFIVPLRDSETHMPLPGVDIGEIGKKL
GMASVNQGFLGLNQVRIPRTNMLMKFAKVERDGTFKASPASRINYLTMVY
TRCLIVSQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
LFPEIATGIAYHLATEYVWEMYDQTVQEANNGKFERLPDMHILSCALKVL
CTTDGCAGIERLRLSTGGHGYLTAANLSNIYGNAVAAYTYEGENTVLLLQ
IGRALVKAWASFVEKKPLSASYSYFATSMQLKEFPKWDDSWQCIIKALQY
TAAQKPRIAFENLANRMASGQSQGVAANNTGIELTRAAELHGRQFVCQTF
LEQITGAKAQKRSPALNKILENVLELFLVQTVLNNLNDILRFISLSDADL
RSLQKRLEDSLEQFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
AKRSTMNQKPVQTSFETYLKPLMKAKL
>C6
MSHIKNLIPNTVNPDLQKERTGAEFNVEEFSAWWHGGQDKLKTKREMETA
IFSDLEDGYGLNHEYMSHEEVYNSSIKKVAEAATKLKALQQKLNPGGKDI
WPGGLFNAQSFGLFPANHPIATHITMFVDVIKGQGTPEQVQKWGPAAENC
NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
GHTANHAMVVAQLYIADVHHGVQMFIVPLRDSETHLPLPGVDIGEIGKKL
GMASVNQGFLGLNNVRIPRTNMLMKFAKVESDGTFKASPASRLNYLTMVY
TRCLIVNQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
LFPEIATGMAYFLAAEYTWDMYAQTVEEANNGKFDRLPEMHILSCALKVL
CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAITYEGENTVLLLQ
IGRALVKAWSSFVENKPLSASYGYFATSMKLKEFPKWDNSWECIIKALQY
TAAQKTRIAYENLAERMLSGQSQGVAANNTGIELTRAAELHGRQFVCQTF
LEQITGPKAQKRSAALNKVLENVLELFLVQTVLNNLNDILRFINLTDADL
RSLQKRLEVSLENFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
AKRSTMNQKPVQNSFETYLKPLMKAKL
>C7
MSHIKNLIPNTVNPDLQKERTGAEFNVEEFSAWWHGGQDKLKTKREMEAA
IFSDLEDGYGLNHEYMSHEEVYNSSIKKVAEAATKLKALQNKLNPGGKDI
WPGGLYNAQSFGLFPANHPVATHITMFVDVIKGQGTPEQVEKWGPAAQNC
NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
GHTANHAMVVAQLYIADVHHGVQMFIVPVRDAETHLPLPGIDIGEIGKKL
GMASVNQGFLGLNNVRIPRTNMLMKFAKVEKDGTFKASPASRLNYLTMVY
TRCLIVNQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
LFPEIATGMAYHMAAEYTWEMYAQTVEEANKGKFDRLPEMHILSCALKVL
CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAITYEGENTVLLLQ
IGRALVKAWSSFVENKPLSASYGYFATSMQLKEFPKWDNSWQCIIKALQY
TAAQKTRIAYENLAERMLSGQSQGVAANNTGIELTRAAELHGRQFVCQTF
LEQITGPKAQKRSSALNKILENVLELFLVQTVLNNLNEILRFINLTDADL
RSLQKRLEVSLEKFRPNAVAVCDGFEFHDRVLNSVLGSYDGNVYPRLFDS
AKRSTMNQKPVQNSFETYLKPLMKAKL
>C8
MSHIKNLIPNTVNPDLQKERTGAEFNVKEFSAWWHGGQGKLKTKREIETA
IFSDLEDGYGIDHEYMSHEEVYNSSVKKVAEAATKLKALQNKLNPGGNDI
WPGVLFNAQSFGLFPANHPVATHITMFVDVIKGQGTPEQVEKWGKAAENC
NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
GHTANHAMVVAQLYIGDVHHGVQMFIVPVRDAETHMPLPGIDIGEIGKKL
GMASVNQGFLGMNNVRIPRTNMLMKFAKVERDGTFKASPASKLNYLTMVY
TRCLIVNLNSTLLLASATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
LFPEIATGMAYHLAAEYMWEIYAQTVQEANSGKFDRLPDMHVLSCALKVL
CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAYTYEGENTVLLLQ
IGRALVKAWASFEENKPVSASYSYFATSMKLKEFPKWDDSWQCIIKALQY
TAAHKTRIAFENLANRMISGQSQGVAANNTGIELTRAAELHGRQFVCQTF
LEQITGPKAQKRSPALNKVLENVLELFLVQTVLNNLNDVLRFISLSDADL
RSLQKRLEVSLEKFRPNAVAICDGFEFHDRVLNSVLGCYDGNVYPRLFDS
AKRSTMNQKPVQKSFETYLKPLMKANL
>C9
MSHIKNLIPNTVNPDLQKERTGAEFNVEEFSAWWQGGQDKLKTKREIEKA
IFSDLEDGYGIDHEYMSHEEVYNSSVKKVADAAIKLKALQNKLNPGGNDI
WPGVLFNVHSHGLFPANHPVATHITMFVDVIKGQGTPEQVEKWGKAAENC
NIIGTYAQTELAHGTNVRGIATRADFDPKTDEFVMHTPNLEAYKWWPGGL
GHTANHAMVVAQLYIADVHHGVQMFIVPVRDAETHMPLPGIDIGEIGKKL
GMVSVNQGFLGLNQVRIPRTNMLMKFAKVERDGTFKASPASRVNYLTMVY
TRCLIVNLNSTLLLEAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
LFPEIANGMAYHLAAEHMWEMYAQTVQEANNGKFDRLPDMHILSCALKVL
CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAYTYEGENTVLLLQ
IGRALVKAWASFVEKKPLSASYSYFATSMQLKEFPKWDNSWQCIIKALQY
TAAQKTRIAFENLANRMASGQSQGVAANNTGIELVRAAELHGRQFVCQTF
LEQITGAKAQKRSAALNKVLENVLELFLVQTVLNNLNDILRFINLTDADL
RSLQKRLEVSLEKFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
AKRSTMNQKPVQKSFETYLKPLMKANL
>C10
MSHIKNLIPNTVNPDLQKERTGAEFSVEEFSAWWHGGQDKLKTKREMEKA
IFSDLEDGYGLNHEYMSHEEVYNSSVKKVAEAAIKLKALQQKLNPGGTDI
WPGGLFNAQSFGLFPANHPVATHITMFVDVIKGQGTPEQVEKWGKAAANC
NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
GHTANHAMVVAQLYIADVHHGIQMFIVPVRDAETHMPLPGIDIGEIGKKL
GMASVNQGFLGMNQVRIPRTNMLMKFAKVERDGTFKASPASRLNYLTMVY
TRCLIVNQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
LFPEIATGMAYHLAAEYTWEMYAQTVQEANNGKFDRLPDMHVLSCALKVL
CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAITYEGENTVLLLQ
IGRALVKAWSSFVEGKPLSASYGYFATSMQLKEFPKWDDSWQCIIKALQY
TAAQKTRIAFENLAERMVSGQSQGVAANNTGIELTRAAELHGRQFVCQTF
LEQITGPKAQKRSPALNKVLENVLELFLVQTVLNNLNEILRFINLTDADL
RSLQKRLEVSLENFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
AKRSTMNQKPVQTSFETHLKPLMKANL
CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=100, Nseq=10, Len=677 

C1              MSHIKNLIPSTVNPDLQKERAAAEFHVEEFSAWWHGGQDKLKKKREIEKA
C2              MSHIKNLIPSTVNPFLQKERAEAEFNVEEFSAWWHGGQDKLKKKREIEKA
C3              MSHIKNLIPSTVNPDLQKERSAAEFNVEEFSAWWHGGQDKLKKKREIEKA
C4              MSHIKNLIPSTVNPDLQKERTGAEFDVEEFSAWWHGGQDKLKRKREIEEA
C5              MSHIKNLIPSTVNPDLQKERTGAEFNVEEFSAWWHGGQDKLKKKREIEKA
C6              MSHIKNLIPNTVNPDLQKERTGAEFNVEEFSAWWHGGQDKLKTKREMETA
C7              MSHIKNLIPNTVNPDLQKERTGAEFNVEEFSAWWHGGQDKLKTKREMEAA
C8              MSHIKNLIPNTVNPDLQKERTGAEFNVKEFSAWWHGGQGKLKTKREIETA
C9              MSHIKNLIPNTVNPDLQKERTGAEFNVEEFSAWWQGGQDKLKTKREIEKA
C10             MSHIKNLIPNTVNPDLQKERTGAEFSVEEFSAWWHGGQDKLKTKREMEKA
                *********.**** *****: *** *:******:***.*** ***:* *

C1              IFSDLEDGYGLNHEYMSHEEVYNSTVKKVAEAAVKLKALQNKLNPGGTDI
C2              IFSDLEDGYGLNHEYMSHEEVYNSTVKKVAEASVKLKALQNKLNPGGTDI
C3              IFSDLEDGYGLNHEYMSHEEVYNSTVKKVAEAAVKLKALQNKLNPGGTDI
C4              IFSDLEDGYGLNHEYMSHEEVYNSTVKKVAEAAVKLKALQNKLNPGGTDI
C5              LFSDLEDGYGLNHEYMSHEEVYNSSVKKVAEAAVKLKALQNKLNPGGTDI
C6              IFSDLEDGYGLNHEYMSHEEVYNSSIKKVAEAATKLKALQQKLNPGGKDI
C7              IFSDLEDGYGLNHEYMSHEEVYNSSIKKVAEAATKLKALQNKLNPGGKDI
C8              IFSDLEDGYGIDHEYMSHEEVYNSSVKKVAEAATKLKALQNKLNPGGNDI
C9              IFSDLEDGYGIDHEYMSHEEVYNSSVKKVADAAIKLKALQNKLNPGGNDI
C10             IFSDLEDGYGLNHEYMSHEEVYNSSVKKVAEAAIKLKALQQKLNPGGTDI
                :*********::************::****:*: ******:******.**

C1              WPGGLFNAQSFGLFPANHPIATHITMFVDVIKGQGTAEQVEKWGKAAENC
C2              WPGGLFNAQSFGLFPANHPVATHITMFVDVIKGQGTAEQVEKWGKPAENC
C3              WPGGLFNAQSFGLFPANHPVATHITMFVDVIKGQGTAEQVEKWGKAAENC
C4              WPGGLYNAQSYGLFPANHPVATHITMFVDVIKGQGTAEQAEKWGKAAANC
C5              WPGGLFNAQSFGLFPANHPVATHITMFVDVIKGQGTPEQVEKWGKAAENC
C6              WPGGLFNAQSFGLFPANHPIATHITMFVDVIKGQGTPEQVQKWGPAAENC
C7              WPGGLYNAQSFGLFPANHPVATHITMFVDVIKGQGTPEQVEKWGPAAQNC
C8              WPGVLFNAQSFGLFPANHPVATHITMFVDVIKGQGTPEQVEKWGKAAENC
C9              WPGVLFNVHSHGLFPANHPVATHITMFVDVIKGQGTPEQVEKWGKAAENC
C10             WPGGLFNAQSFGLFPANHPVATHITMFVDVIKGQGTPEQVEKWGKAAANC
                *** *:*.:*.********:****************.**.:*** .* **

C1              NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
C2              NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
C3              NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
C4              NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
C5              NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
C6              NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
C7              NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
C8              NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
C9              NIIGTYAQTELAHGTNVRGIATRADFDPKTDEFVMHTPNLEAYKWWPGGL
C10             NIIGTYAQTELAHGTNVRGLATRADFDPKTDEFVLNTPNLEAYKWWPGGL
                *******************:**************::**************

C1              GHTANHAMVVAQLYIADVHHGVQMFIVPLRDSETHMPLPGVDIGEIGKKL
C2              GHTANHAMVVAQLYIADVHHGVQMFIVPVRDSETHMALPGVDIGEIGKKL
C3              GHTANHAMVVAQLYIADVHHGVQMFIVPVRDSETHMPLPGVDIGEIGKKL
C4              GHTANHAMVVAQLYIADVHHGVQMFIVPLRDSETHMPLPGVDIGEVGKKL
C5              GHTANHAMVVAQLYIADVHHGVQMFIVPLRDSETHMPLPGVDIGEIGKKL
C6              GHTANHAMVVAQLYIADVHHGVQMFIVPLRDSETHLPLPGVDIGEIGKKL
C7              GHTANHAMVVAQLYIADVHHGVQMFIVPVRDAETHLPLPGIDIGEIGKKL
C8              GHTANHAMVVAQLYIGDVHHGVQMFIVPVRDAETHMPLPGIDIGEIGKKL
C9              GHTANHAMVVAQLYIADVHHGVQMFIVPVRDAETHMPLPGIDIGEIGKKL
C10             GHTANHAMVVAQLYIADVHHGIQMFIVPVRDAETHMPLPGIDIGEIGKKL
                ***************.*****:******:**:***:.***:****:****

C1              GMASVNQGFLGLNHVRIPRTNMLMKFAKVERDGTFKASPASRINYLTMVY
C2              GMASVNQGFLGLNHVRIPRTNMLMKFAKVERDGTFKASPASRINYLTMVY
C3              GMASVNQGFLGLNHVRIPRTNMLMKFAKVERDGTFKASPASRINYLTMVY
C4              GMASVNQGFLGLDHVRIPRTNMLMKFAKVERDGTFKASPASRINYLTMVY
C5              GMASVNQGFLGLNQVRIPRTNMLMKFAKVERDGTFKASPASRINYLTMVY
C6              GMASVNQGFLGLNNVRIPRTNMLMKFAKVESDGTFKASPASRLNYLTMVY
C7              GMASVNQGFLGLNNVRIPRTNMLMKFAKVEKDGTFKASPASRLNYLTMVY
C8              GMASVNQGFLGMNNVRIPRTNMLMKFAKVERDGTFKASPASKLNYLTMVY
C9              GMVSVNQGFLGLNQVRIPRTNMLMKFAKVERDGTFKASPASRVNYLTMVY
C10             GMASVNQGFLGMNQVRIPRTNMLMKFAKVERDGTFKASPASRLNYLTMVY
                **.********:::**************** **********::*******

C1              TRCLIVSQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
C2              TRCLIVSQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
C3              TRCLIVSQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
C4              TRCLIVSQNSMLHLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
C5              TRCLIVSQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
C6              TRCLIVNQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
C7              TRCLIVNQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
C8              TRCLIVNLNSTLLLASATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
C9              TRCLIVNLNSTLLLEAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
C10             TRCLIVNQNSTLLLAAATIATRYSAVRRQSPIEPNQPEPQIIDHVTQRLK
                ******. ** * * :**********************************

C1              LFPEIATGIAYHLATEYMWEMYAQTVQEANNGKFERLPDMHILSCALKVL
C2              LFPEIATGIAYHLATEYVWEMYAQTVQEANNGKFERLPDMHILSCALKVL
C3              LFPEIATGIAYHLATEYVWEMYAQTVQEANNGKFERLPDMHILSCALKVL
C4              LFPEIATGIAYHLATEYVWEMYDQTVLEANNGKFERLPDMHILSCALKVL
C5              LFPEIATGIAYHLATEYVWEMYDQTVQEANNGKFERLPDMHILSCALKVL
C6              LFPEIATGMAYFLAAEYTWDMYAQTVEEANNGKFDRLPEMHILSCALKVL
C7              LFPEIATGMAYHMAAEYTWEMYAQTVEEANKGKFDRLPEMHILSCALKVL
C8              LFPEIATGMAYHLAAEYMWEIYAQTVQEANSGKFDRLPDMHVLSCALKVL
C9              LFPEIANGMAYHLAAEHMWEMYAQTVQEANNGKFDRLPDMHILSCALKVL
C10             LFPEIATGMAYHLAAEYTWEMYAQTVQEANNGKFDRLPDMHVLSCALKVL
                ******.*:**.:*:*: *::* *** ***.***:***:**:********

C1              CTTDGCAGIEKLRLSTGGHGYLIAANLSNIYGNAVAAYTYEGENTVLLLQ
C2              CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAYTYEGENTVLLLQ
C3              CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAYTYEGENTVLLLQ
C4              CTTDGCAGIERLRLSTGGHGYLIAANLSNIYGNAVAAYTYEGENTVLLLQ
C5              CTTDGCAGIERLRLSTGGHGYLTAANLSNIYGNAVAAYTYEGENTVLLLQ
C6              CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAITYEGENTVLLLQ
C7              CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAITYEGENTVLLLQ
C8              CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAYTYEGENTVLLLQ
C9              CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAYTYEGENTVLLLQ
C10             CTTDGCAGIEKLRLSTGGHGYLTAANLSNIYGNAVAAITYEGENTVLLLQ
                **********:*********** ************** ************

C1              IGRALVKAWASFVDKKPLSASYSYFASSMQLKEFPKWDDSWQCIIKALQY
C2              IGRALVKAWASFVDKKPLSASYSYFASSMQLKEFPKWDDSWQCIIKALQY
C3              IGRALVKAWASFVDKKPLSASYSYFASSMQLKEFPKWDDSWQCIIKALQY
C4              IGRALVKAWASFVEQKPLSASYSYFATSMQLKEFPKWDDSWQCIIKALQY
C5              IGRALVKAWASFVEKKPLSASYSYFATSMQLKEFPKWDDSWQCIIKALQY
C6              IGRALVKAWSSFVENKPLSASYGYFATSMKLKEFPKWDNSWECIIKALQY
C7              IGRALVKAWSSFVENKPLSASYGYFATSMQLKEFPKWDNSWQCIIKALQY
C8              IGRALVKAWASFEENKPVSASYSYFATSMKLKEFPKWDDSWQCIIKALQY
C9              IGRALVKAWASFVEKKPLSASYSYFATSMQLKEFPKWDNSWQCIIKALQY
C10             IGRALVKAWSSFVEGKPLSASYGYFATSMQLKEFPKWDDSWQCIIKALQY
                *********:** : **:****.***:**:********:**:********

C1              TAAHKTRIAFENLANRMASGQSQGVAANNTGIELTRAAELHGRQFVCQTF
C2              TAAHKTRIAFENLANRMASGQSQGVAANNTGIELTRAAELHGRQFVCQTF
C3              TAAHKTRIAFENLANRMASGQSQGVAANNTGIELTRAAELHGRQFVCQTF
C4              TAAHKTRIAFENLANRMASGQSQGAAANNTGIELTRAAELHGRQFVCQTF
C5              TAAQKPRIAFENLANRMASGQSQGVAANNTGIELTRAAELHGRQFVCQTF
C6              TAAQKTRIAYENLAERMLSGQSQGVAANNTGIELTRAAELHGRQFVCQTF
C7              TAAQKTRIAYENLAERMLSGQSQGVAANNTGIELTRAAELHGRQFVCQTF
C8              TAAHKTRIAFENLANRMISGQSQGVAANNTGIELTRAAELHGRQFVCQTF
C9              TAAQKTRIAFENLANRMASGQSQGVAANNTGIELVRAAELHGRQFVCQTF
C10             TAAQKTRIAFENLAERMVSGQSQGVAANNTGIELTRAAELHGRQFVCQTF
                ***:*.***:****:** ******.*********.***************

C1              LEQITGAKAQKRSPALNKILENVLELFLVQTVLNNLNDILRFIKLSDADL
C2              LEQITGAKAQKRSPALNKILENVLELFLVQTVLNNLNDILRFIKLSDADL
C3              LEQITGAKAQKRSPALNKILENVLELFLVQTVLNNLNDILRFIQLSDADL
C4              LEQITGAKAQKRSPALNRILENVLELFLVQTVLNNLNDILRFINLSDADL
C5              LEQITGAKAQKRSPALNKILENVLELFLVQTVLNNLNDILRFISLSDADL
C6              LEQITGPKAQKRSAALNKVLENVLELFLVQTVLNNLNDILRFINLTDADL
C7              LEQITGPKAQKRSSALNKILENVLELFLVQTVLNNLNEILRFINLTDADL
C8              LEQITGPKAQKRSPALNKVLENVLELFLVQTVLNNLNDVLRFISLSDADL
C9              LEQITGAKAQKRSAALNKVLENVLELFLVQTVLNNLNDILRFINLTDADL
C10             LEQITGPKAQKRSPALNKVLENVLELFLVQTVLNNLNEILRFINLTDADL
                ******.******.***::******************::****.*:****

C1              RSLQKRLEDSLAQFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
C2              RSLQKRLEDSLEQFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
C3              RSLQRRLEDSLEQFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
C4              RSLQKRLEDALERFRPNAVAICDGFGFHDRVLNSVLGSYDGNVYPRLFDS
C5              RSLQKRLEDSLEQFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
C6              RSLQKRLEVSLENFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
C7              RSLQKRLEVSLEKFRPNAVAVCDGFEFHDRVLNSVLGSYDGNVYPRLFDS
C8              RSLQKRLEVSLEKFRPNAVAICDGFEFHDRVLNSVLGCYDGNVYPRLFDS
C9              RSLQKRLEVSLEKFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
C10             RSLQKRLEVSLENFRPNAVAICDGFEFHDRVLNSVLGSYDGNVYPRLFDS
                ****:*** :* .*******:**** ***********.************

C1              AKRSTMNQKPVQTSFETYLKPLMKAKL
C2              AKRSTMNQKPVQTSFESYLKPLMKAKL
C3              AKRSTMNQKPVQTSFETYLKPLMKAKL
C4              AKRSTMNQKPVQTSFETHLKPLMKAKL
C5              AKRSTMNQKPVQTSFETYLKPLMKAKL
C6              AKRSTMNQKPVQNSFETYLKPLMKAKL
C7              AKRSTMNQKPVQNSFETYLKPLMKAKL
C8              AKRSTMNQKPVQKSFETYLKPLMKANL
C9              AKRSTMNQKPVQKSFETYLKPLMKANL
C10             AKRSTMNQKPVQTSFETHLKPLMKANL
                ************.***::*******:*




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/3/Acox57D-d-PA/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/3/Acox57D-d-PA/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/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  677 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:
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/3/Acox57D-d-PA/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/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  677 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnplugins       	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/3/Acox57D-d-PA/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/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  677 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnplugins       	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/3/Acox57D-d-PA/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/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  677 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnplugins       	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/3/Acox57D-d-PA/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/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  677 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  677 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnplugins       	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/3/Acox57D-d-PA/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/3/Acox57D-d-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  677 type PROTE