; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/cad.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/cad_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/cad.tab
; Output files
;	output	html_ready/cad_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : cad
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	3	1	7	8	9	9	7
c	|	7	6	0	1	2	1	0	0
g	|	3	1	2	2	0	0	1	0
t	|	0	0	7	0	0	0	0	3
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	10	10	10	10	10	10	10	10	80
; c.max	|	7	6	7	7	8	9	9	7	9
; c.min	|	0	0	0	0	0	0	0	0	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	0	7	3	0	|	10	 0.70	 0.89	C	S	CCCCCCggg
2	3	6	1	0	|	10	 0.60	 0.53	C	C	aCCC
3	1	0	2	7	|	10	 0.70	 0.34	t	k	gtt
4	7	1	2	0	|	10	 0.70	 0.37	a	r	aac
5	8	2	0	0	|	10	 0.80	 0.55	a	m	aaaaac
6	9	1	0	0	|	10	 0.90	 0.64	a	a	aaaaaaac
7	9	0	1	0	|	10	 0.90	 0.64	a	a	aaaaaaag
8	7	0	0	3	|	10	 0.70	 0.36	a	a	aat
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	| -0.1 -0.0 -0.1  0.5  0.6  0.8  0.8  0.5
c	|  0.9  0.7 -0.0 -0.0  0.0 -0.0 -0.0 -0.0
g	|  0.2 -0.0  0.0  0.0 -0.0 -0.0 -0.0 -0.0
t	| -0.1 -0.1  0.5 -0.1 -0.1 -0.1 -0.1 -0.0
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.9  0.5  0.3  0.4  0.5  0.6  0.6  0.4  4.3
; i.max	|  0.9  0.7  0.5  0.5  0.6  0.8  0.8  0.5  0.9
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1
; Sites	10
>cad_chr3R_2689568_268958
cctaaaaa
>cad_chr3L_20631266_20631
cctaaaaa
>cad_chr3L_20631349_20631
cataaaaa
>cad_chr3R_2689641_268966
cataaaaa
>cad_chr3L_20631445_20631
gcggaaaa
>cad_chr2L_11455703_11455
gcgacaat
>cad_chr2L_11455958_11455
gctcaaat
>cad_chr3L_20631297_20631
cgtgcaaa
>cad_chr3L_20631388_20631
ccaaacaa
>cad_chr3L_20631325_20631
cataaagt
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.332|c:0.168|g:0.168|t:0.332
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/cad_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	10
;	meme.llr                     	57
;	meme.E-value                 	46
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.168
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.32018
;	information.per.column       	0.540023
;	max.possible.info.per.col    	1.78379
;	consensus.strict             	CCtaaaaa
;	consensus.strict.rc          	tttttaGG
;	consensus.IUPAC              	SCkrmaaa
;	consensus.IUPAC.rc           	tttkymGS
;	consensus.regexp             	[CG]C[gt][ag][ac]aaa
;	consensus.regexp.rc          	ttt[gt][ct][ac]G[CG]
;	residues.content.crude.freq  	a:0.5500|c:0.2125|g:0.1125|t:0.1250
;	G+C.content.crude.freq       	0.325
;	residues.content.corrected.freq	a:0.5302|c:0.2085|g:0.1175|t:0.1438
;	G+C.content.corrected.freq   	0.326
;	min(P(S|M))                  	2.28465e-14
;	max(P(S|M))                  	0.0589884
;	proba_range                  	0.0589884
;	Wmin                         	-19.2
;	Wmax                         	7.4
;	Wrange                       	26.6
; Job started 2007_12_10.132043
; Job done    2007_12_10.132043