--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Nov 22 08:16:58 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-PG/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

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

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -2466.01         -2484.91
2      -2465.92         -2491.75
--------------------------------------
TOTAL    -2465.97         -2491.06
--------------------------------------


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

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.405539    0.004198    0.287953    0.537082    0.399629   1151.96   1285.41    1.000
r(A<->C){all}   0.135157    0.001324    0.065472    0.205019    0.132245    877.62    912.21    1.003
r(A<->G){all}   0.206237    0.002191    0.117848    0.294669    0.203357    583.12    664.68    1.000
r(A<->T){all}   0.133072    0.001700    0.058529    0.215591    0.130242    669.94    793.30    1.003
r(C<->G){all}   0.055255    0.000306    0.023688    0.089028    0.053444   1026.52   1064.14    1.001
r(C<->T){all}   0.460926    0.003745    0.334927    0.575895    0.460106    605.01    629.37    1.000
r(G<->T){all}   0.009354    0.000077    0.000002    0.027146    0.006739   1150.86   1162.94    1.001
pi(A){all}      0.238435    0.000155    0.214425    0.262464    0.238015   1259.68   1344.98    1.001
pi(C){all}      0.304132    0.000167    0.278019    0.327796    0.303839   1147.97   1263.61    1.000
pi(G){all}      0.266757    0.000166    0.242084    0.292463    0.266671    965.01   1073.51    1.001
pi(T){all}      0.190677    0.000114    0.171532    0.212362    0.190658   1110.73   1157.09    1.000
alpha{1,2}      0.114328    0.000420    0.076541    0.151545    0.112923   1317.52   1381.32    1.000
alpha{3}        2.162042    0.600672    0.844509    3.652757    2.026815   1261.18   1302.66    1.001
pinvar{all}     0.743327    0.000778    0.683516    0.790727    0.744759   1393.53   1412.02    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	-2366.016141
Model 2: PositiveSelection	-2364.894727
Model 0: one-ratio	-2386.440429
Model 3: discrete	-2364.894727
Model 7: beta	-2371.804541
Model 8: beta&w>1	-2364.902852


Model 0 vs 1	40.84857600000032

Model 2 vs 1	2.2428280000003724

Model 8 vs 7	13.803377999999611

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-PG)

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

    46 S      0.999**       2.319
    47 S      0.996**       2.313
    48 C      0.994**       2.309
    49 D      0.999**       2.318
    51 L      1.000**       2.322

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-PG)

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

    46 S      0.856         1.899 +- 1.059
    47 S      0.740         1.670 +- 1.072
    48 C      0.680         1.534 +- 1.039
    49 D      0.811         1.786 +- 1.019
    51 L      0.868         1.894 +- 0.992

>C1
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
LAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHGHSAVHH
PVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALAN
LKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRR
DPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL
KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C2
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
LAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHGHSAVHH
PVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALAN
LKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRR
DPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL
KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C3
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
LAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHGHSAVHH
PVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALAN
LKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRR
DPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL
KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C4
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
LAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHGHSAVHH
PVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALAN
LKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRR
DPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL
KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C5
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
LAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHGHSAVHH
PVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALAN
LKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRR
DPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL
KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C6
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
LAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHGHSAVHH
PVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALAN
LKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRR
DPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL
KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C7
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SLESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
LAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHGHSAVHH
PVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALAN
LKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRR
DPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL
KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C8
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SIESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
LAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHGHSAVHH
PVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALAN
LKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRR
DPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL
KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C9
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIYTHHLPS
FQSRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQAQ
HVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTTL
APISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHGHSAVHHP
VITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALANL
KLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRRD
PDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLK
KNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGYo
>C10
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SIESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
LAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHGHSAVHH
PVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALAN
LKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRR
DPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL
KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
>C11
MTMSMYSTTDKMKMSAPSCFPGRYSPSYRSSEQMRRCMPNPSIHISSSCD
SIESRLLEDASLLCNSWSARQNGDIFAGINDGILSRAEALAAVDIQKHQA
QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
LAPISESPLTPTHQHLHGSYHSMNHMMSHHHPGTLSGHTGGHHGHSAVHH
PVITAAVAAAGLHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALAN
LKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKNKRR
DPDAPSVLPAGEKKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL
KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY
CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=100, Nseq=11, Len=388 

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              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
C2              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
C3              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
C4              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
C5              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
C6              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
C7              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
C8              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
C9              QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
C10             QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
C11             QHVHSQMPSQIKHDVMYHHHSMSGPPQRPLQMHHSMDQLDMLDPTGSMTT
                **************************************************

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

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

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

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

C1              KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C2              KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C3              KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C4              KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C5              KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C6              KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C7              KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C8              KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C9              KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGYo
C10             KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
C11             KKNVVRVWFCNQRQKQKRIVSSVTPSMTGHGSAGFGY-
                ************************************* 




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/acj6-PG/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_threshol