PROGRAM: T-COFFEE (Version_2.11)
-run_name      	S	[1] 	/usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598
-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 
-seq           	S	[0] 
-in            	S	[1] 	/usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.in0	Mlalign_id_pair	Mslow_pair	Msap_pair	Mfugue_pair
-pdb           	S	[0] 
-out_lib       	W_F	[1] 	no
-outseqweight  	W_F	[0] 	no
-seq_to_align  	S	[0] 
-cosmetic_penalty	D	[0] 	-50 
-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
-usetree       	R_F	[0] 
-tree_mode     	S	[0] 	slow
-quicktree     	FL	[0] 	0
-outfile       	W_F	[0] 	default
-maximise      	FL	[1] 	1
-output        	S	[1] 	clustalw_aln	score_pdf	fasta_aln	score_ascii	score_html
-infile        	R_F	[0] 
-matrix        	S	[0] 
-tg_mode       	D	[0] 	1 
-profile_mode  	S	[0] 	cw_profile_profile
-profile_comparison	S	[0] 	full50
-dp_mode       	S	[0] 	cfasta_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
-type          	S	[0] 
-outorder      	S	[1] 	input
-seqnos        	S	[1] 	on
-case          	S	[1] 	lower
-cpu           	D	[0] 	0 
-maxnseq       	D	[1] 	50 
-maxlen        	D	[1] 	2000 
-weight        	S	[0] 	sim
-seq_weight    	S	[0] 	no
-align         	FL	[1] 	1
-mocca         	FL	[0] 	0
-start         	D	[0] 	0 
-len           	D	[0] 	0 
-scale         	D	[0] 	0 
-mocca_interactive	FL	[0] 	0
-evaluate_mode 	S	[1] 	t_coffee_slow
-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
-profile       	S	[0] 
-profile1      	S	[0] 
-profile2      	S	[0] 
-extend_matrix 	FL	[0] 	0
-prot_min_sim  	D	[40] 	40 
-prot_max_sim  	D	[60] 	60 
-prot_min_cov  	D	[0] 	0 
-pdb_min_sim   	D	[30] 	30 
-pdb_max_sim   	D	[100] 	100 
-pdb_min_cov   	D	[50] 	50 
-pdb_blast_server	W_F	[0] 	SIB
-prot_blast_server	W_F	[0] 	SIB
-pdb_db        	W_F	[0] 	nrl3d
-protein_db    	W_F	[0] 	nr
-method_log    	W_F	[0] 	no
-struc_to_use  	S	[0] 
-cache         	W_F	[1] 	no
-align_pdb_param_file	W_F	[0] 	no
-align_pdb_hasch_mode	W_F	[0] 	hasch_ca_trace_bubble
-msa_mode      	S	[0] 	tree
-lalign_n_top  	D	[0] 	10 
-iterate       	D	[0] 	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	[1] 	1 
-seq_to_keep   	S	[0] 

INPUT FILES
	Input File (S) /usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.in0  Format fasta_seq
	Input File (M) lalign_id_pair 
	Input File (M) slow_pair 
	Input File (M) sap_pair 
	Input File (M) fugue_pair 

INPUT SEQUENCES: 4 SEQUENCES  [PROTEIN]
	Input File /usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.in0 Seq 1ajsA Length  365 type PROTEIN Struct Yes PDBID 1AJS
	Input File /usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.in0 Seq 2dkb  Length  380 type PROTEIN Struct Yes PDBID 2DKB
	Input File /usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.in0 Seq 2gsaA Length  365 type PROTEIN Struct Yes PDBID 2GSA
	Input File /usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.in0 Seq 1ax4A Length  387 type PROTEIN Struct Yes PDBID 1AX4

READ/MAKE LIBRARIES:[5]

	lalign_id_pair [method]

		[TOT=    6][  0 %]
		[TOT=    6][ 33 %]
		[TOT=    6][ 50 %]
		[TOT=    6][ 66 %]
		[TOT=    6][ 83 %]
		[TOT=    6][100 %]
	slow_pair [method]

		[TOT=    6][  0 %]
		[TOT=    6][ 33 %]
		[TOT=    6][ 50 %]
		[TOT=    6][ 66 %]
		[TOT=    6][ 83 %]
		[TOT=    6][100 %]
	sap_pair [method]

		[TOT=    6][  0 %]
		[TOT=    6][ 33 %]
		[TOT=    6][ 50 %]
		[TOT=    6][ 66 %]
		[TOT=    6][ 83 %]
		[TOT=    6][100 %]
	fugue_pair [method]

		[TOT=    6][  0 %]
		[TOT=    6][ 33 %]
		[TOT=    6][ 50 %]
		[TOT=    6][ 66 %]
		[TOT=    6][ 83 %]
		[TOT=    6][100 %]

	Library Total Size: [4797]


UN-WEIGHTED MODE: EVERY SEQUENCE WEIGHTS 1

COMPUTE PAIRWISE SIMILARITY [dp_mode: cfasta_pair_wise] [tree_mode: slow] 

	1ajsA 1ax4A identity=  9% score= 30
	1ajsA 2dkb  identity=  9% score= 31
	1ajsA 2gsaA identity=  8% score= 31
	1ax4A 2dkb  identity= 11% score= 28
	1ax4A 2gsaA identity= 12% score= 29
	2dkb  2gsaA identity= 20% score= 40
MAKE NEIGHBOR JOINING DENDROGRAM
	[MODE=slow][DONE]

PROGRESSIVE_ALIGNMENT [Tree Based]

	Group   5: [Group   3 (  1 seq)] with [Group   4 (  1 seq)]-->[Score=  17][Len=  389]
	Group   6: [Group   5 (  2 seq)] with [Group   1 (  1 seq)]-->[Score=  30][Len=  417]
	Group   7: [Group   2 (  1 seq)] with [Group   6 (  3 seq)]-->[Score=  42][Len=  444]



OUTPUT RESULTS
	#### File Type=       TREE Format=      newik Name= /usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.dnd
	#### File Type=        MSA Format= clustalw_aln Name= /usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.clustalw_aln
	#### File Type=        MSA Format=  score_pdf Name= /usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.score_pdf
	#### File Type=        MSA Format=  fasta_aln Name= /usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.fasta_aln
	#### File Type=        MSA Format= score_ascii Name= /usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.score_ascii
	#### File Type=        MSA Format= score_html Name= /usr/local/httpd/htdocs/Tcoffee/Tmp/tcfAA99504_23598.score_html


T-COFFEE Memory Usage: Current= 3.929 Mb, Max= 6.426 Mb

T-COFFEE CPU Usage: 8150 millisec