; convert-matrix  -v 1 -i /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PutA/PutA_2rbf_AB.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PutA/PutA_2rbf_AB.tab/PutA_2rbf_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 PutA_2rbf_AB '
; Input files
;	input	/export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PutA/PutA_2rbf_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/PutA/PutA_2rbf_AB.tab/PutA_2rbf_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	|	0	24	14	7	51	96	0	0
c	|	0	24	9	59	14	0	96	96
g	|	96	24	51	14	17	0	0	0
t	|	0	24	22	16	14	0	0	0
//
a	|  0.0  0.3  0.1  0.1  0.5  1.0  0.0  0.0
c	|  0.0  0.2  0.1  0.6  0.1  0.0  1.0  1.0
g	|  1.0  0.2  0.5  0.1  0.2  0.0  0.0  0.0
t	|  0.0  0.3  0.2  0.2  0.1  0.0  0.0  0.0
//
a	| -4.6 -0.2 -0.7 -1.4  0.6  1.2 -4.6 -4.6
c	| -4.6  0.2 -0.8  1.1 -0.3 -4.6  1.6  1.6
g	|  1.6  0.2  0.9 -0.3 -0.1 -4.6 -4.6 -4.6
t	| -4.6 -0.2 -0.3 -0.6 -0.7 -4.6 -4.6 -4.6
//
a	| -0.0 -0.0 -0.1 -0.1  0.3  1.2 -0.0 -0.0
c	| -0.0  0.0 -0.1  0.7 -0.1 -0.0  1.6  1.6
g	|  1.6  0.0  0.5 -0.0 -0.0 -0.0 -0.0 -0.0
t	| -0.0 -0.0 -0.1 -0.1 -0.1 -0.0 -0.0 -0.0
//
; 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            	6.57515
;	information.per.column       	0.821893
;	max.possible.info.per.col    	1.5879
;	consensus.strict             	GggCaACC
;	consensus.strict.rc          	GGTTGCCC
;	consensus.IUPAC              	GsgCaACC
;	consensus.IUPAC.rc           	GGTTGCSC
;	consensus.regexp             	G[cg]gCaACC
;	consensus.regexp.rc          	GGTTGC[CG]C
;	residues.content.crude.freq  	a:0.2500|c:0.3880|g:0.2630|t:0.0990
;	G+C.content.crude.freq       	0.651042
;	residues.content.corrected.freq	a:0.2504|c:0.3862|g:0.2624|t:0.1010
;	G+C.content.corrected.freq   	0.648575
;	min(P(S|M))                  	5.21277e-15
;	max(P(S|M))                  	0.0413337
;	proba_range                  	0.0413337
;	Wmin                         	-21.4
;	Wmax                         	8.9
;	Wrange                       	30.3
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PutA/PutA_2rbf_AB.tab/PutA_2rbf_AB_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PutA/PutA_2rbf_AB.tab/PutA_2rbf_AB_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PutA/PutA_2rbf_AB.tab/PutA_2rbf_AB_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PutA/PutA_2rbf_AB.tab/PutA_2rbf_AB_m1_logo_rc.pdf
; Job started 2010_03_11.202051
; Job done    2010_03_11.202054