--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Dec 09 08:53:17 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/428/tzn-PB/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/428/tzn-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/428/tzn-PB/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/428/tzn-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3192.62         -3207.98
2      -3192.65         -3207.07
--------------------------------------
TOTAL    -3192.63         -3207.62
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/428/tzn-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/428/tzn-PB/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/428/tzn-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.447938    0.015773    1.215993    1.708439    1.441083   1342.63   1366.96    1.000
r(A<->C){all}   0.133379    0.000454    0.094602    0.175631    0.131964   1070.45   1137.80    1.000
r(A<->G){all}   0.228824    0.000938    0.173451    0.290681    0.226899    785.23    794.96    1.000
r(A<->T){all}   0.052116    0.000419    0.015139    0.093646    0.050618    717.94    903.61    1.000
r(C<->G){all}   0.050766    0.000119    0.029241    0.071332    0.050201   1118.63   1163.23    1.000
r(C<->T){all}   0.445580    0.001496    0.367161    0.517688    0.445607    704.64    792.75    1.000
r(G<->T){all}   0.089335    0.000322    0.055458    0.126661    0.088776    920.40   1020.90    1.000
pi(A){all}      0.229106    0.000202    0.202244    0.258663    0.228826   1004.00   1079.80    1.001
pi(C){all}      0.292770    0.000210    0.265912    0.322918    0.292240    951.22   1041.39    1.000
pi(G){all}      0.305481    0.000241    0.276005    0.337460    0.305356   1201.36   1250.16    1.001
pi(T){all}      0.172643    0.000136    0.149235    0.195023    0.172476   1072.19   1099.75    1.000
alpha{1,2}      0.134949    0.000180    0.111796    0.163796    0.133963   1331.82   1387.56    1.000
alpha{3}        3.260841    0.716636    1.763059    4.903222    3.149239   1136.87   1318.93    1.000
pinvar{all}     0.297314    0.001842    0.210226    0.377163    0.298613   1428.28   1464.64    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	-2923.991963
Model 2: PositiveSelection	-2923.991963
Model 0: one-ratio	-2962.937232
Model 3: discrete	-2918.649864
Model 7: beta	-2925.314041
Model 8: beta&w>1	-2921.899747


Model 0 vs 1	77.89053800000056

Model 2 vs 1	0.0

Model 8 vs 7	6.828588000000309

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
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_tzn-PB)

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

    32 T      0.664         1.304 +- 0.678

>C1
MHSTLEDVQLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
TVQEQQLTLSKVLTTHHHWDHAGGNEKLLKLWEKELDVYGGDDRIGALNK
KVQQDDTFTIGGLHVKCLSTPCHTTGHICYHITAQQGSGEGAVFTGDTLF
QGGCGRFFEGTPEEMYEALCTKLSALPDATKVFCGHEYTLQNMSFARHVE
PDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKHAG
GATDPVVTMGKLRKEKDTFKAoo
>C2
MHSTLEDVQLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
TVQEQQLTLSKVLTTHHHWDHAGGNEKLLKLWQKELDVYGGDDRIGALNK
KVQQDDTFTIGGLHVKCLSTPCHTTGHICYHVTAQDGSGEGAVFTGDTLF
QGGCGRFFEGTPEEMYEALCTKLSALPDATKVFCGHEYTLQNMSFARHVE
PDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEAAVQKHAG
GATDPVVTMGKLRKEKDTFKAoo
>C3
MHSTLEDVQLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
TVQEQQLTLSKVLTTHHHWDHAGGNEKLLKLWQKELDVYGGDDRIGALNK
KVQQDDTFTIGGLHVKCLSTPCHTTGHICYHVTAQDGSGEGAVFTGDTLF
QGGCGRFFEGTPEEMYEALCTKLSALPDATKVFCGHEYTLQNMSFARHVE
PDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKHAG
GATDPVVTMGKLRKEKDTFKAoo
>C4
MHSTVEDVKLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
TLQEQQLTLSKVLTTHHHWDHAGGNEKLVKLWEKELDVYGGDDRIGALNK
KVQQDDTFTIGALNVKCLSTPCHTTGHICYHVTAQEGSGKGAVFTGDTLF
QGGCGRFFEGTPEEMYEALCTKLSSLPDTTKVFCGHEYTLQNMSFARHVE
PDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEASVQKHAG
GATDPIVTMGKLRKEKDTFKAoo
>C5
MHSTLEDVKLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
TVQEEQLTLNKVLTTHHHWDHAGGNEKLVKLWEKQLDVYGGDDRIGALNH
KVKQDDTLTIGSLKVKCLSTPCHTTGHICYHVTAQDGGGGEGAVFTGDTL
FQGGCGRFFEGTPEEMYEALCTKLSALPDGTKVFCGHEYTLQNMSFARHV
EPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKHA
GGATDPIVTMGKLRKEKDNFKAo
>C6
MHSTLEDVKLEGMEIKILPALQDNYMYLIVDRKTREAAVVDPVEPELVIK
TVQEEQLTLSKVLTTHHHWDHAGGNEKLVKLWDGKQLDVYGGDDRIGALN
QKVQQDDTFSIGSLNVKCLSTPCHTTGHICYHVTAQDGSGGEGAVFTGDT
LFQGGCGRFFEGTPEEMYEALCTKLSALPDGTKVFCGHEYTLQNMSFARH
VEPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKH
AGGATDPIVTMGKLRKEKDNFKA
>C7
MHSTLEDVKLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
TVQEEKLTLNKVLTTHHHWDHAGGNEKLVKLWDKQLDVYGGDDRIGALNQ
KVQQDDTFTIGSLNVKCLSTPCHTTGHICYHVTSQEGSGEGAVFTGDTLF
QGGCGRFFEGTPEEMYEALCTKLSALPDTTKVFCGHEYTLQNMSFARHVE
PDNEVIQQRIEWAKHRRAAQDPTVPSTIGEEKSWNPFMRVHEATVQKHAG
GATDPIITMGKLRKEKDTFKAoo
>C8
MHSTLEDVKLEGMEIKILPALQDNYMYLIVDGKTREAAVVDPVEPELVIK
TVQEEKLTLKKVLTTHHHWDHAGGNEKLVKLWEQQLDVYGGDDRIGALNK
KVQQDDTFTIGSLNVKCLSTPCHTTGHICYHVTAQDGNGEGAVFTGDTLF
QGGCGRFFEGTPDEMYEALCTKLSALPDSTKVFCGHEYTLQNMSFARHVE
PDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKHAG
GATDPIVTMGKLRKEKDNFKAoo
>C9
MHSTTEAVKLEGMEIKILPALQDNYMYLIVDAKTREAAVVDPVDPELVIK
TVQDEQLTLSKVLTTHHHWDHAGGNEKLVKLWEKQLDVYGGDDRIGALNQ
KVQQDDSFTIGSLNVKCLSTPCHTTGHICYHVTAGGGNGEGAVFTGDTLF
QGGCGRFFEGTPEEMYEALCTKLSALPDNTKVFCGHEYTLQNMSFARHVE
PDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKHAG
GATDPIVTMGKLRKEKDNFKAoo
>C10
MHSTLEDVKLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
TVQEEQLTLNKVLTTHHHWDHAGGNEKLVKLWEKQLDVYGGDDRIGALNQ
KVQQDDSFTIGSLNVKCLSTPCHTTGHICYHVTAGDGSGEGAVFTGDTLF
QGGCGRFFEGTAEEMYEALCTKLSALPDDTKVFCGHEYTLQNMSFARHVE
PDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKHAG
GATDPIVTMGKLRKEKDTFKAoo
>C11
MHSTLEDVKLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
TVQEEQLTLNKVLTTHHHWDHAGGNEKLVKLWEKQLDVYGGDDRIGALNQ
KVQQDDTFTIGSLNVKCLSTPCHTTGHICYHVTAQEGGEGAVFTGDTLFQ
GGCGRFFEGTPEEMYEALCTKLSALPDATKVFCGHEYTLQNMSFARHVEP
DNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEETVQKHAGG
DTDPIVTMGKLRKEKDTFKAooo
CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=100, Nseq=11, Len=276 

C1              MHSTLEDVQLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
C2              MHSTLEDVQLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
C3              MHSTLEDVQLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
C4              MHSTVEDVKLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
C5              MHSTLEDVKLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
C6              MHSTLEDVKLEGMEIKILPALQDNYMYLIVDRKTREAAVVDPVEPELVIK
C7              MHSTLEDVKLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
C8              MHSTLEDVKLEGMEIKILPALQDNYMYLIVDGKTREAAVVDPVEPELVIK
C9              MHSTTEAVKLEGMEIKILPALQDNYMYLIVDAKTREAAVVDPVDPELVIK
C10             MHSTLEDVKLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
C11             MHSTLEDVKLEGMEIKILPALQDNYMYLIVDTKTREAAVVDPVEPELVIK
                **** * *:********************** ***********:******

C1              TVQEQQLTLSKVLTTHHHWDHAGGNEKLLKLWE-KELDVYGGDDRIGALN
C2              TVQEQQLTLSKVLTTHHHWDHAGGNEKLLKLWQ-KELDVYGGDDRIGALN
C3              TVQEQQLTLSKVLTTHHHWDHAGGNEKLLKLWQ-KELDVYGGDDRIGALN
C4              TLQEQQLTLSKVLTTHHHWDHAGGNEKLVKLWE-KELDVYGGDDRIGALN
C5              TVQEEQLTLNKVLTTHHHWDHAGGNEKLVKLWE-KQLDVYGGDDRIGALN
C6              TVQEEQLTLSKVLTTHHHWDHAGGNEKLVKLWDGKQLDVYGGDDRIGALN
C7              TVQEEKLTLNKVLTTHHHWDHAGGNEKLVKLWD-KQLDVYGGDDRIGALN
C8              TVQEEKLTLKKVLTTHHHWDHAGGNEKLVKLWE-QQLDVYGGDDRIGALN
C9              TVQDEQLTLSKVLTTHHHWDHAGGNEKLVKLWE-KQLDVYGGDDRIGALN
C10             TVQEEQLTLNKVLTTHHHWDHAGGNEKLVKLWE-KQLDVYGGDDRIGALN
C11             TVQEEQLTLNKVLTTHHHWDHAGGNEKLVKLWE-KQLDVYGGDDRIGALN
                *:*:::***.******************:***: ::**************

C1              KKVQQDDTFTIGGLHVKCLSTPCHTTGHICYHITAQQGSG-EGAVFTGDT
C2              KKVQQDDTFTIGGLHVKCLSTPCHTTGHICYHVTAQDGSG-EGAVFTGDT
C3              KKVQQDDTFTIGGLHVKCLSTPCHTTGHICYHVTAQDGSG-EGAVFTGDT
C4              KKVQQDDTFTIGALNVKCLSTPCHTTGHICYHVTAQEGSG-KGAVFTGDT
C5              HKVKQDDTLTIGSLKVKCLSTPCHTTGHICYHVTAQDGGGGEGAVFTGDT
C6              QKVQQDDTFSIGSLNVKCLSTPCHTTGHICYHVTAQDGSGGEGAVFTGDT
C7              QKVQQDDTFTIGSLNVKCLSTPCHTTGHICYHVTSQEGSG-EGAVFTGDT
C8              KKVQQDDTFTIGSLNVKCLSTPCHTTGHICYHVTAQDGNG-EGAVFTGDT
C9              QKVQQDDSFTIGSLNVKCLSTPCHTTGHICYHVTAGGGNG-EGAVFTGDT
C10             QKVQQDDSFTIGSLNVKCLSTPCHTTGHICYHVTAGDGSG-EGAVFTGDT
C11             QKVQQDDTFTIGSLNVKCLSTPCHTTGHICYHVTAQEG-G-EGAVFTGDT
                :**:***:::**.*:*****************:*:  * * :********

C1              LFQGGCGRFFEGTPEEMYEALCTKLSALPDATKVFCGHEYTLQNMSFARH
C2              LFQGGCGRFFEGTPEEMYEALCTKLSALPDATKVFCGHEYTLQNMSFARH
C3              LFQGGCGRFFEGTPEEMYEALCTKLSALPDATKVFCGHEYTLQNMSFARH
C4              LFQGGCGRFFEGTPEEMYEALCTKLSSLPDTTKVFCGHEYTLQNMSFARH
C5              LFQGGCGRFFEGTPEEMYEALCTKLSALPDGTKVFCGHEYTLQNMSFARH
C6              LFQGGCGRFFEGTPEEMYEALCTKLSALPDGTKVFCGHEYTLQNMSFARH
C7              LFQGGCGRFFEGTPEEMYEALCTKLSALPDTTKVFCGHEYTLQNMSFARH
C8              LFQGGCGRFFEGTPDEMYEALCTKLSALPDSTKVFCGHEYTLQNMSFARH
C9              LFQGGCGRFFEGTPEEMYEALCTKLSALPDNTKVFCGHEYTLQNMSFARH
C10             LFQGGCGRFFEGTAEEMYEALCTKLSALPDDTKVFCGHEYTLQNMSFARH
C11             LFQGGCGRFFEGTPEEMYEALCTKLSALPDATKVFCGHEYTLQNMSFARH
                *************.:***********:*** *******************

C1              VEPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKH
C2              VEPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEAAVQKH
C3              VEPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKH
C4              VEPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEASVQKH
C5              VEPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKH
C6              VEPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKH
C7              VEPDNEVIQQRIEWAKHRRAAQDPTVPSTIGEEKSWNPFMRVHEATVQKH
C8              VEPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKH
C9              VEPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKH
C10             VEPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEATVQKH
C11             VEPDNEVIQQRIEWAKHRRASQDPTVPSTIGEEKSWNPFMRVHEETVQKH
                ********************:*********************** :****

C1              AGGATDPVVTMGKLRKEKDTFKAoo-
C2              AGGATDPVVTMGKLRKEKDTFKAoo-
C3              AGGATDPVVTMGKLRKEKDTFKAoo-
C4              AGGATDPIVTMGKLRKEKDTFKAoo-
C5              AGGATDPIVTMGKLRKEKDNFKAo--
C6              AGGATDPIVTMGKLRKEKDNFKA---
C7              AGGATDPIITMGKLRKEKDTFKAoo-
C8              AGGATDPIVTMGKLRKEKDNFKAoo-
C9              AGGATDPIVTMGKLRKEKDNFKAoo-
C10             AGGATDPIVTMGKLRKEKDTFKAoo-
C11             AGGDTDPIVTMGKLRKEKDTFKAooo
                *** ***::**********.***   




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/428/tzn-PB/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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:
ins       	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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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/428/tzn-PB/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: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  273 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  273 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/428/tzn-PB/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnins       	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