; convert-matrix  -v 1 -i /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/Ada/Ada_1zgw_A.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Ada/Ada_1zgw_A.tab/Ada_1zgw_A.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 Ada_1zgw_A '
; Input files
;	input	/export/internal_use2/amedina/matrix_eval/data/Matrices_contact/Ada/Ada_1zgw_A.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/Ada/Ada_1zgw_A.tab/Ada_1zgw_A.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	|	16	0	0	0	0	24	24	0	8	96	96	0
c	|	8	0	0	96	0	24	24	16	8	0	0	0
g	|	16	0	96	0	96	24	24	16	8	0	0	0
t	|	56	96	0	0	0	24	24	64	72	0	0	96
//
a	|  0.2  0.0  0.0  0.0  0.0  0.3  0.3  0.0  0.1  1.0  1.0  0.0
c	|  0.1  0.0  0.0  1.0  0.0  0.2  0.2  0.2  0.1  0.0  0.0  0.0
g	|  0.2  0.0  1.0  0.0  1.0  0.2  0.2  0.2  0.1  0.0  0.0  0.0
t	|  0.6  1.0  0.0  0.0  0.0  0.3  0.3  0.7  0.7  0.0  0.0  1.0
//
a	| -0.5 -4.6 -4.6 -4.6 -4.6 -0.2 -0.2 -4.6 -1.2  1.2  1.2 -4.6
c	| -0.9 -4.6 -4.6  1.6 -4.6  0.2  0.2 -0.2 -0.9 -4.6 -4.6 -4.6
g	| -0.2 -4.6  1.6 -4.6  1.6  0.2  0.2 -0.2 -0.9 -4.6 -4.6 -4.6
t	|  0.7  1.2 -4.6 -4.6 -4.6 -0.2 -0.2  0.8  0.9 -4.6 -4.6  1.2
//
a	| -0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1  1.2  1.2 -0.0
c	| -0.1 -0.0 -0.0  1.6 -0.0  0.0  0.0 -0.0 -0.1 -0.0 -0.0 -0.0
g	| -0.0 -0.0  1.6 -0.0  1.6  0.0  0.0 -0.0 -0.1 -0.0 -0.0 -0.0
t	|  0.4  1.2 -0.0 -0.0 -0.0 -0.0 -0.0  0.5  0.7 -0.0 -0.0  1.2
//
; Sites	
;
; Matrix parameters
;	Columns                      	12
;	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            	10.3664
;	information.per.column       	0.86387
;	max.possible.info.per.col    	1.5879
;	consensus.strict             	tTGCGggttAAT
;	consensus.strict.rc          	ATTAACCCGCAA
;	consensus.IUPAC              	tTGCGssttAAT
;	consensus.IUPAC.rc           	ATTAASSCGCAA
;	consensus.regexp             	tTGCG[cg][cg]ttAAT
;	consensus.regexp.rc          	ATTAA[CG][CG]CGCAA
;	residues.content.crude.freq  	a:0.2292|c:0.1528|g:0.2431|t:0.3750
;	G+C.content.crude.freq       	0.395833
;	residues.content.corrected.freq	a:0.2298|c:0.1533|g:0.2427|t:0.3742
;	G+C.content.corrected.freq   	0.395997
;	min(P(S|M))                  	2.53629e-25
;	max(P(S|M))                  	0.0170471
;	proba_range                  	0.0170471
;	Wmin                         	-39.2
;	Wmax                         	12.5
;	Wrange                       	51.7
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Ada/Ada_1zgw_A.tab/Ada_1zgw_A_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Ada/Ada_1zgw_A.tab/Ada_1zgw_A_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Ada/Ada_1zgw_A.tab/Ada_1zgw_A_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Ada/Ada_1zgw_A.tab/Ada_1zgw_A_m1_logo_rc.pdf
; Job started 2010_03_12.110520
; Job done    2010_03_12.110525