; convert-matrix  -v 1 -i /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/LacI/LacI_1efa_AB.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/LacI/LacI_1efa_AB.tab/LacI_1efa_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 LacI_1efa_AB '
; Input files
;	input	/export/internal_use2/amedina/matrix_eval/data/Matrices_contact/LacI/LacI_1efa_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/LacI/LacI_1efa_AB.tab/LacI_1efa_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	|	3	0	0	6	78	65	0	0	6	6	6	78	0	96	75
c	|	3	0	0	0	6	6	96	0	81	1	87	0	96	0	6
g	|	5	96	0	89	3	22	0	96	3	0	0	18	0	0	9
t	|	85	0	96	1	9	3	0	0	6	89	3	0	0	0	6
//
a	|  0.0  0.0  0.0  0.1  0.8  0.7  0.0  0.0  0.1  0.1  0.1  0.8  0.0  1.0  0.8
c	|  0.0  0.0  0.0  0.0  0.1  0.1  1.0  0.0  0.8  0.0  0.9  0.0  1.0  0.0  0.1
g	|  0.1  1.0  0.0  0.9  0.0  0.2  0.0  1.0  0.0  0.0  0.0  0.2  0.0  0.0  0.1
t	|  0.9  0.0  1.0  0.0  0.1  0.0  0.0  0.0  0.1  0.9  0.0  0.0  0.0  0.0  0.1
//
a	| -2.1 -4.6 -4.6 -1.5  1.0  0.8 -4.6 -4.6 -1.5 -1.5 -1.5  1.0 -4.6  1.2  1.0
c	| -1.8 -4.6 -4.6 -4.6 -1.2 -1.2  1.6 -4.6  1.4 -2.8  1.5 -4.6  1.6 -4.6 -1.2
g	| -1.3  1.6 -4.6  1.5 -1.8  0.1 -4.6  1.6 -1.8 -4.6 -4.6 -0.1 -4.6 -4.6 -0.8
t	|  1.1 -4.6  1.2 -3.1 -1.1 -2.2 -4.6 -4.6 -1.5  1.1 -2.2 -4.6 -4.6 -4.6 -1.5
//
a	| -0.1 -0.0 -0.0 -0.1  0.8  0.6 -0.0 -0.0 -0.1 -0.1 -0.1  0.8 -0.0  1.2  0.8
c	| -0.1 -0.0 -0.0 -0.0 -0.1 -0.1  1.6 -0.0  1.2 -0.0  1.3 -0.0  1.6 -0.0 -0.1
g	| -0.1  1.6 -0.0  1.4 -0.1  0.0 -0.0  1.6 -0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1
t	|  1.0 -0.0  1.2 -0.0 -0.1 -0.1 -0.0 -0.0 -0.1  1.0 -0.1 -0.0 -0.0 -0.0 -0.1
//
; Sites	
;
; Matrix parameters
;	Columns                      	15
;	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            	15.6872
;	information.per.column       	1.04581
;	max.possible.info.per.col    	1.5879
;	consensus.strict             	TGTGAaCGCTCACAa
;	consensus.strict.rc          	TTGTGAGCGTTCACA
;	consensus.IUPAC              	TGTGArCGCTCACAa
;	consensus.IUPAC.rc           	TTGTGAGCGYTCACA
;	consensus.regexp             	TGTGA[ag]CGCTCACAa
;	consensus.regexp.rc          	TTGTGAGCG[CT]TCACA
;	residues.content.crude.freq  	a:0.2910|c:0.2653|g:0.2368|t:0.2069
;	G+C.content.crude.freq       	0.502083
;	residues.content.corrected.freq	a:0.2910|c:0.2647|g:0.2365|t:0.2079
;	G+C.content.corrected.freq   	0.501152
;	min(P(S|M))                  	1.4336e-34
;	max(P(S|M))                  	0.181869
;	proba_range                  	0.181869
;	Wmin                         	-55.3
;	Wmax                         	19.3
;	Wrange                       	74.6
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/LacI/LacI_1efa_AB.tab/LacI_1efa_AB_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/LacI/LacI_1efa_AB.tab/LacI_1efa_AB_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/LacI/LacI_1efa_AB.tab/LacI_1efa_AB_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/LacI/LacI_1efa_AB.tab/LacI_1efa_AB_m1_logo_rc.pdf
; Job started 2010_03_12.110611
; Job done    2010_03_12.110654