; convert-matrix  -v 1 -i /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/Rob/Rob_1d5y_AB.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Rob/Rob_1d5y_AB.tab/Rob_1d5y_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 Rob_1d5y_AB '
; Input files
;	input	/export/internal_use2/amedina/matrix_eval/data/Matrices_contact/Rob/Rob_1d5y_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/Rob/Rob_1d5y_AB.tab/Rob_1d5y_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	|	14	34	6	0	74	14
c	|	52	20	6	96	8	52
g	|	16	22	78	0	7	14
t	|	14	20	6	0	7	16
//
a	|  0.1  0.4  0.1  0.0  0.8  0.1
c	|  0.5  0.2  0.1  1.0  0.1  0.5
g	|  0.2  0.2  0.8  0.0  0.1  0.1
t	|  0.1  0.2  0.1  0.0  0.1  0.2
//
a	| -0.7  0.2 -1.5 -4.6  1.0 -0.7
c	|  1.0  0.0 -1.2  1.6 -0.9  1.0
g	| -0.2  0.1  1.4 -4.6 -1.0 -0.3
t	| -0.7 -0.4 -1.5 -4.6 -1.4 -0.6
//
a	| -0.1  0.1 -0.1 -0.0  0.7 -0.1
c	|  0.5  0.0 -0.1  1.6 -0.1  0.5
g	| -0.0  0.0  1.1 -0.0 -0.1 -0.0
t	| -0.1 -0.1 -0.1 -0.0 -0.1 -0.1
//
; Sites	
;
; Matrix parameters
;	Columns                      	6
;	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            	3.40323
;	information.per.column       	0.567204
;	max.possible.info.per.col    	1.5879
;	consensus.strict             	caGCac
;	consensus.strict.rc          	GTGCTG
;	consensus.IUPAC              	cvGCac
;	consensus.IUPAC.rc           	GTGCBG
;	consensus.regexp             	c[acg]GCac
;	consensus.regexp.rc          	GTGC[CGT]G
;	residues.content.crude.freq  	a:0.2465|c:0.4062|g:0.2378|t:0.1094
;	G+C.content.crude.freq       	0.644097
;	residues.content.corrected.freq	a:0.2470|c:0.4042|g:0.2375|t:0.1113
;	G+C.content.corrected.freq   	0.641702
;	min(P(S|M))                  	4.50043e-08
;	max(P(S|M))                  	0.0627177
;	proba_range                  	0.0627177
;	Wmin                         	-9.3
;	Wmax                         	6.1
;	Wrange                       	15.4
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Rob/Rob_1d5y_AB.tab/Rob_1d5y_AB_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Rob/Rob_1d5y_AB.tab/Rob_1d5y_AB_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Rob/Rob_1d5y_AB.tab/Rob_1d5y_AB_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Rob/Rob_1d5y_AB.tab/Rob_1d5y_AB_m1_logo_rc.pdf
; Job started 2010_03_11.202959
; Job done    2010_03_11.203003