; convert-matrix  -v 1 -i /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PhoB/PhoB_1gxp_AB.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_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 PhoB_1gxp_AB '
; Input files
;	input	/export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PhoB/PhoB_1gxp_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/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_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	|	6	6	24	12	3	96	0	86	24	0	0	6	0	24	24	6	96	0	96
c	|	81	76	24	12	3	0	96	3	24	96	0	6	0	24	24	6	0	96	0
g	|	3	6	24	12	86	0	0	4	24	0	0	6	0	24	24	78	0	0	0
t	|	6	8	24	60	4	0	0	3	24	0	96	78	96	24	24	6	0	0	0
//
a	|  0.1  0.1  0.3  0.1  0.0  1.0  0.0  0.9  0.3  0.0  0.0  0.1  0.0  0.3  0.3  0.1  1.0  0.0  1.0
c	|  0.8  0.8  0.2  0.1  0.0  0.0  1.0  0.0  0.2  1.0  0.0  0.1  0.0  0.2  0.2  0.1  0.0  1.0  0.0
g	|  0.0  0.1  0.2  0.1  0.9  0.0  0.0  0.0  0.2  0.0  0.0  0.1  0.0  0.2  0.2  0.8  0.0  0.0  0.0
t	|  0.1  0.1  0.3  0.6  0.0  0.0  0.0  0.0  0.3  0.0  1.0  0.8  1.0  0.3  0.3  0.1  0.0  0.0  0.0
//
a	| -1.5 -1.5 -0.2 -0.8 -2.1  1.2 -4.6  1.1 -0.2 -4.6 -4.6 -1.5 -4.6 -0.2 -0.2 -1.5  1.2 -4.6  1.2
c	|  1.4  1.3  0.2 -0.5 -1.8 -4.6  1.6 -1.8  0.2  1.6 -4.6 -1.2 -4.6  0.2  0.2 -1.2 -4.6  1.6 -4.6
g	| -1.8 -1.2  0.2 -0.5  1.5 -4.6 -4.6 -1.6  0.2 -4.6 -4.6 -1.2 -4.6  0.2  0.2  1.4 -4.6 -4.6 -4.6
t	| -1.5 -1.2 -0.2  0.7 -1.9 -4.6 -4.6 -2.2 -0.2 -4.6  1.2  1.0  1.2 -0.2 -0.2 -1.5 -4.6 -4.6 -4.6
//
a	| -0.1 -0.1 -0.0 -0.1 -0.1  1.2 -0.0  1.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.1  1.2 -0.0  1.2
c	|  1.2  1.0  0.0 -0.1 -0.1 -0.0  1.6 -0.1  0.0  1.6 -0.0 -0.1 -0.0  0.0  0.0 -0.1 -0.0  1.6 -0.0
g	| -0.1 -0.1  0.0 -0.1  1.3 -0.0 -0.0 -0.1  0.0 -0.0 -0.0 -0.1 -0.0  0.0  0.0  1.1 -0.0 -0.0 -0.0
t	| -0.1 -0.1 -0.0  0.5 -0.1 -0.0 -0.0 -0.1 -0.0 -0.0  1.2  0.8  1.2 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0
//
; Sites	
;
; Matrix parameters
;	Columns                      	19
;	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            	15.6736
;	information.per.column       	0.824926
;	max.possible.info.per.col    	1.5879
;	consensus.strict             	CCgtGACAgCTtTggGACA
;	consensus.strict.rc          	TGTCCCAAAGCTGTCACGG
;	consensus.IUPAC              	CCstGACAsCTtTssGACA
;	consensus.IUPAC.rc           	TGTCSSAAAGSTGTCASGG
;	consensus.regexp             	CC[cg]tGACA[cg]CTtT[cg][cg]GACA
;	consensus.regexp.rc          	TGTC[CG][CG]AAAG[CG]TGTCA[CG]GG
;	residues.content.crude.freq  	a:0.2791|c:0.3130|g:0.1595|t:0.2484
;	G+C.content.crude.freq       	0.472588
;	residues.content.corrected.freq	a:0.2792|c:0.3120|g:0.1600|t:0.2489
;	G+C.content.corrected.freq   	0.47196
;	min(P(S|M))                  	1.78999e-33
;	max(P(S|M))                  	0.000778995
;	proba_range                  	0.000778995
;	Wmin                         	-48.9
;	Wmax                         	20.1
;	Wrange                       	69
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_AB_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_AB_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_AB_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_AB_m1_logo_rc.pdf
; Job started 2010_03_11.195605
; Job done    2010_03_11.195731