; convert-matrix  -v 1 -i /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/TrpR/TrpR_1rcs_AB.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB.tab_quality_matrix_info.txt -bgfile /export/space2/rsa-tools/data/genomes/Escherichia_coli_K12/oligo-frequencies/1nt_upstream-noorf_Escherichia_coli_K12-ovlp-1str.freq -bg_format oligos -return counts,frequencies,weights,info,parameters,sites,logo -logo_format png,pdf -logo_opt '-e -M -t TrpR_1rcs_AB '
; Input files
;	input	/export/internal_use2/amedina/matrix_eval/data/Matrices_contact/TrpR/TrpR_1rcs_AB.tab
;	prior	/export/space2/rsa-tools/data/genomes/Escherichia_coli_K12/oligo-frequencies/1nt_upstream-noorf_Escherichia_coli_K12-ovlp-1str.freq
; Input format        	tab
; Output files
;	output	/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB.tab_quality_matrix_info.txt
; Output format       	tab
; pseudo-weight       	1
; Background model
;	Bernoulli model (order=0)
;	Strand        	sensitive
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.29107
;		c	0.20737
;		g	0.20436
;		t	0.29721
a	|	0	0	86	0	24	96	4	24	24	24	24	14	7	52	0	0	96	0
c	|	0	0	1	96	24	0	9	24	24	24	24	67	4	14	0	14	0	96
g	|	96	0	9	0	24	0	72	24	24	24	24	9	4	11	96	0	0	0
t	|	0	96	0	0	24	0	11	24	24	24	24	6	81	19	0	82	0	0
//
a	|  0.0  0.0  0.9  0.0  0.3  1.0  0.0  0.3  0.3  0.3  0.3  0.1  0.1  0.5  0.0  0.0  1.0  0.0
c	|  0.0  0.0  0.0  1.0  0.2  0.0  0.1  0.2  0.2  0.2  0.2  0.7  0.0  0.1  0.0  0.1  0.0  1.0
g	|  1.0  0.0  0.1  0.0  0.2  0.0  0.7  0.2  0.2  0.2  0.2  0.1  0.0  0.1  1.0  0.0  0.0  0.0
t	|  0.0  1.0  0.0  0.0  0.3  0.0  0.1  0.3  0.3  0.3  0.3  0.1  0.8  0.2  0.0  0.8  0.0  0.0
//
a	| -4.6 -4.6  1.1 -4.6 -0.2  1.2 -1.9 -0.2 -0.2 -0.2 -0.2 -0.7 -1.4  0.6 -4.6 -4.6  1.2 -4.6
c	| -4.6 -4.6 -2.8  1.6  0.2 -4.6 -0.8  0.2  0.2  0.2  0.2  1.2 -1.6 -0.3 -4.6 -0.3 -4.6  1.6
g	|  1.6 -4.6 -0.8 -4.6  0.2 -4.6  1.3  0.2  0.2  0.2  0.2 -0.8 -1.6 -0.6  1.6 -4.6 -4.6 -4.6
t	| -4.6  1.2 -4.6 -4.6 -0.2 -4.6 -0.9 -0.2 -0.2 -0.2 -0.2 -1.5  1.0 -0.4 -4.6  1.0 -4.6 -4.6
//
a	| -0.0 -0.0  1.0 -0.0 -0.0  1.2 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.1  0.3 -0.0 -0.0  1.2 -0.0
c	| -0.0 -0.0 -0.0  1.6  0.0 -0.0 -0.1  0.0  0.0  0.0  0.0  0.8 -0.1 -0.1 -0.0 -0.1 -0.0  1.6
g	|  1.6 -0.0 -0.1 -0.0  0.0 -0.0  1.0  0.0  0.0  0.0  0.0 -0.1 -0.1 -0.1  1.6 -0.0 -0.0 -0.0
t	| -0.0  1.2 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1  0.9 -0.1 -0.0  0.9 -0.0 -0.0
//
; Sites	
;
; Matrix parameters
;	Columns                      	18
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.291066898814656|c:0.207372933914605|g:0.204355073413807|t:0.297205093856932
;	program                      	tab
;	matrix.nb                    	1
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.204355
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	13.4138
;	information.per.column       	0.745212
;	max.possible.info.per.col    	1.5879
;	consensus.strict             	GTACgAGggggCTaGTAC
;	consensus.strict.rc          	GTACTAGCCCCCTCGTAC
;	consensus.IUPAC              	GTACsAGssssCTaGTAC
;	consensus.IUPAC.rc           	GTACTAGSSSSCTSGTAC
;	consensus.regexp             	GTAC[cg]AG[cg][cg][cg][cg]CTaGTAC
;	consensus.regexp.rc          	GTACTAG[CG][CG][CG][CG]CT[CG]GTAC
;	residues.content.crude.freq  	a:0.2749|c:0.2436|g:0.2413|t:0.2402
;	G+C.content.crude.freq       	0.484954
;	residues.content.corrected.freq	a:0.2751|c:0.2433|g:0.2409|t:0.2408
;	G+C.content.corrected.freq   	0.484199
;	min(P(S|M))                  	1.70313e-32
;	max(P(S|M))                  	0.000164179
;	proba_range                  	0.000164179
;	Wmin                         	-47.7
;	Wmax                         	17.3
;	Wrange                       	65
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB_m1_logo_rc.pdf
; Job started 2010_03_11.203914
; Job done    2010_03_11.204012