--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Nov 22 07:35:47 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/acj6-PD/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/3/acj6-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/acj6-PD/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/acj6-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -2521.38         -2541.31
2      -2520.76         -2542.99
--------------------------------------
TOTAL    -2521.02         -2542.46
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/3/acj6-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/acj6-PD/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/acj6-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.392428    0.003524    0.285761    0.512680    0.387646   1266.95   1383.97    1.001
r(A<->C){all}   0.138435    0.001432    0.072093    0.219702    0.134902    622.52    739.30    1.000
r(A<->G){all}   0.213541    0.002195    0.125547    0.308132    0.211593    760.58    838.19    1.000
r(A<->T){all}   0.116765    0.001423    0.052652    0.196236    0.114165    591.59    676.53    1.000
r(C<->G){all}   0.058811    0.000349    0.025840    0.095250    0.056630   1134.72   1134.93    1.000
r(C<->T){all}   0.463083    0.003738    0.348382    0.588857    0.463206    654.12    742.32    1.000
r(G<->T){all}   0.009366    0.000076    0.000001    0.026225    0.006913    926.49    962.41    1.000
pi(A){all}      0.238697    0.000141    0.217082    0.262326    0.238344   1230.92   1251.61    1.000
pi(C){all}      0.303027    0.000162    0.276742    0.326906    0.303178   1257.35   1283.09    1.000
pi(G){all}      0.264913    0.000157    0.239428    0.287742    0.265082   1275.69   1314.71    1.000
pi(T){all}      0.193363    0.000115    0.173782    0.215610    0.193178   1055.53   1271.72    1.000
alpha{1,2}      0.112065    0.000459    0.075590    0.155651    0.110480   1423.83   1424.10    1.000
alpha{3}        2.252867    0.597020    1.027224    3.877691    2.135668   1252.56   1351.75    1.000
pinvar{all}     0.732891    0.000854    0.672830    0.787357    0.734194   1163.38   1332.19    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	-2414.55962
Model 2: PositiveSelection	-2413.472377
Model 0: one-ratio	-2434.934737
Model 3: discrete	-2413.472377
Model 7: beta	-2420.353886
Model 8: beta&w>1	-2413.479913


Model 0 vs 1	40.75023400000009

Model 2 vs 1	2.174485999999888

Model 8 vs 7	13.747945999999502

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_acj6-PD)

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

    46 S      0.999**       2.315
    47 S      0.996**       2.309
    48 C      0.995**       2.306
    49 D      0.999**       2.315
    51 L      1.000**       2.318

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: D_melanogaster_acj6-PD)

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

    46 S      0.853         1.859 +- 1.035
    47 S      0.737         1.634 +- 1.045
    48 C      0.686         1.523 +- 1.019
    49 D      0.811         1.757 +- 0.997
    51 L      0.873         1.870 +- 0.969

>C1
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C2
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C3
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C4
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C5
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C6
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C7
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C8
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SIESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C9
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIYTHHLPS
FQSRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQAQ
HVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLDP
TGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHG
HSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADV
GKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQ
AKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAI
AEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGYo
>C10
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SIESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C11
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SIESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=100, Nseq=11, Len=395 

C1              MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
C2              MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
C3              MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
C4              MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
C5              MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
C6              MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
C7              MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
C8              MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
C9              MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIYT-HHLP
C10             MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
C11             MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
                *******************************************:      

C1              SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
C2              SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
C3              SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
C4              SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
C5              SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
C6              SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
C7              SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
C8              SIESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
C9              SFQSRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
C10             SIESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
C11             SIESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
                *::***********************************************

C1              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
C2              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
C3              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
C4              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
C5              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
C6              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
C7              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
C8              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
C9              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
C10             QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
C11             QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQENPFSRQMHHSMDQLDMLD
                **************************************************

C1              PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
C2              PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
C3              PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
C4              PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
C5              PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
C6              PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
C7              PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
C8              PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
C9              PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
C10             PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
C11             PTGSMTTLAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHH
                **************************************************

C1              GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
C2              GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
C3              GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
C4              GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
C5              GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
C6              GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
C7              GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
C8              GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
C9              GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
C10             GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
C11             GHSAVHHPVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQAD
                **************************************************

C1              VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
C2              VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
C3              VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
C4              VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
C5              VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
C6              VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
C7              VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
C8              VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
C9              VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
C10             VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
C11             VGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA
                **************************************************

C1              QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
C2              QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
C3              QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
C4              QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
C5              QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
C6              QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
C7              QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
C8              QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
C9              QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
C10             QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
C11             QAKNKRRDPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAA
                **************************************************

C1              IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C2              IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C3              IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C4              IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C5              IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C6              IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C7              IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C8              IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C9              IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGYo
C10             IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C11             IAEKLDLKKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
                ******************************************** 




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 
-filte