; convert-matrix  -v 1 -i /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/FadR/FadR_1hw2_AB.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/FadR/FadR_1hw2_AB.tab/FadR_1hw2_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 FadR_1hw2_AB '
; Input files
;	input	/export/internal_use2/amedina/matrix_eval/data/Matrices_contact/FadR/FadR_1hw2_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/FadR/FadR_1hw2_AB.tab/FadR_1hw2_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	|	4	0	0	10	9	0	4	74	0	0	86
c	|	4	0	0	13	65	96	1	9	96	96	2
g	|	6	96	96	9	13	0	91	9	0	0	4
t	|	82	0	0	64	9	0	0	4	0	0	4
//
a	|  0.0  0.0  0.0  0.1  0.1  0.0  0.0  0.8  0.0  0.0  0.9
c	|  0.0  0.0  0.0  0.1  0.7  1.0  0.0  0.1  1.0  1.0  0.0
g	|  0.1  1.0  1.0  0.1  0.1  0.0  0.9  0.1  0.0  0.0  0.0
t	|  0.8  0.0  0.0  0.7  0.1  0.0  0.0  0.0  0.0  0.0  0.0
//
a	| -1.9 -4.6 -4.6 -1.0 -1.1 -4.6 -1.9  1.0 -4.6 -4.6  1.1
c	| -1.6 -4.6 -4.6 -0.4  1.2  1.6 -2.8 -0.8  1.6  1.6 -2.2
g	| -1.2  1.6  1.6 -0.8 -0.4 -4.6  1.5 -0.8 -4.6 -4.6 -1.6
t	|  1.0 -4.6 -4.6  0.8 -1.1 -4.6 -4.6 -1.9 -4.6 -4.6 -1.9
//
a	| -0.1 -0.0 -0.0 -0.1 -0.1 -0.0 -0.1  0.7 -0.0 -0.0  1.0
c	| -0.1 -0.0 -0.0 -0.1  0.8  1.6 -0.0 -0.1  1.6  1.6 -0.1
g	| -0.1  1.6  1.6 -0.1 -0.1 -0.0  1.4 -0.1 -0.0 -0.0 -0.1
t	|  0.9 -0.0 -0.0  0.5 -0.1 -0.0 -0.0 -0.1 -0.0 -0.0 -0.1
//
; Sites	
;
; Matrix parameters
;	Columns                      	11
;	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            	11.6868
;	information.per.column       	1.06244
;	max.possible.info.per.col    	1.5879
;	consensus.strict             	TGGtCCGaCCA
;	consensus.strict.rc          	TGGTCGGACCA
;	consensus.IUPAC              	TGGtCCGaCCA
;	consensus.IUPAC.rc           	TGGTCGGACCA
;	consensus.regexp             	TGGtCCGaCCA
;	consensus.regexp.rc          	TGGTCGGACCA
;	residues.content.crude.freq  	a:0.1771|c:0.3617|g:0.3068|t:0.1544
;	G+C.content.crude.freq       	0.668561
;	residues.content.corrected.freq	a:0.1783|c:0.3602|g:0.3058|t:0.1558
;	G+C.content.corrected.freq   	0.665913
;	min(P(S|M))                  	5.20426e-23
;	max(P(S|M))                  	0.232443
;	proba_range                  	0.232443
;	Wmin                         	-35.7
;	Wmax                         	14.6
;	Wrange                       	50.3
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/FadR/FadR_1hw2_AB.tab/FadR_1hw2_AB_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/FadR/FadR_1hw2_AB.tab/FadR_1hw2_AB_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/FadR/FadR_1hw2_AB.tab/FadR_1hw2_AB_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/FadR/FadR_1hw2_AB.tab/FadR_1hw2_AB_m1_logo_rc.pdf
; Job started 2010_03_11.182753
; Job done    2010_03_11.182759