; convert-matrix  -v 1 -i /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/DnaA/DnaA_1j1v_A.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_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 DnaA_1j1v_A '
; Input files
;	input	/export/internal_use2/amedina/matrix_eval/data/Matrices_contact/DnaA/DnaA_1j1v_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/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_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	|	0	0	0	0	19	96	0	28
c	|	0	0	0	0	11	0	19	9
g	|	0	96	0	96	57	0	0	11
t	|	96	0	96	0	9	0	77	48
//
a	|  0.0  0.0  0.0  0.0  0.2  1.0  0.0  0.3
c	|  0.0  0.0  0.0  0.0  0.1  0.0  0.2  0.1
g	|  0.0  1.0  0.0  1.0  0.6  0.0  0.0  0.1
t	|  1.0  0.0  1.0  0.0  0.1  0.0  0.8  0.5
//
a	| -4.6 -4.6 -4.6 -4.6 -0.4  1.2 -4.6  0.0
c	| -4.6 -4.6 -4.6 -4.6 -0.6 -4.6 -0.0 -0.8
g	| -4.6  1.6 -4.6  1.6  1.1 -4.6 -4.6 -0.6
t	|  1.2 -4.6  1.2 -4.6 -1.1 -4.6  1.0  0.5
//
a	| -0.0 -0.0 -0.0 -0.0 -0.1  1.2 -0.0  0.0
c	| -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.1
g	| -0.0  1.6 -0.0  1.6  0.6 -0.0 -0.0 -0.1
t	|  1.2 -0.0  1.2 -0.0 -0.1 -0.0  0.8  0.3
//
; Sites	
;
; Matrix parameters
;	Columns                      	8
;	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            	7.81527
;	information.per.column       	0.976908
;	max.possible.info.per.col    	1.5879
;	consensus.strict             	TGTGGAtt
;	consensus.strict.rc          	AATCCACA
;	consensus.IUPAC              	TGTGGAtw
;	consensus.IUPAC.rc           	WATCCACA
;	consensus.regexp             	TGTGGAt[at]
;	consensus.regexp.rc          	[AT]ATCCACA
;	residues.content.crude.freq  	a:0.1862|c:0.0508|g:0.3385|t:0.4245
;	G+C.content.crude.freq       	0.389323
;	residues.content.corrected.freq	a:0.1873|c:0.0524|g:0.3372|t:0.4232
;	G+C.content.corrected.freq   	0.389554
;	min(P(S|M))                  	8.19144e-19
;	max(P(S|M))                  	0.225187
;	proba_range                  	0.225187
;	Wmin                         	-29.5
;	Wmax                         	9.5
;	Wrange                       	39
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_A_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_A_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_A_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_A_m1_logo_rc.pdf
; Job started 2010_03_11.181839
; Job done    2010_03_11.181843