; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ems.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/ems_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ems.tab
; Output files
;	output	html_ready/ems_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : ems
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	3	0	0	3	0	3
c	|	0	0	0	0	2	0
g	|	0	0	2	0	1	0
t	|	0	3	1	0	0	0
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	3	3	3	3	3	3	18
; c.max	|	3	3	2	3	2	3	3
; c.min	|	0	0	0	0	0	0	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	3	0	0	0	|	3	 1.00	 0.49	a	a	aaaaa
2	0	0	0	3	|	3	 1.00	 0.49	t	t	ttttt
3	0	0	2	1	|	3	 0.67	 0.52	G	G	GGtt
4	3	0	0	0	|	3	 1.00	 0.49	a	a	aaaaa
5	0	2	1	0	|	3	 0.67	 0.67	C	S	CCCgg
6	3	0	0	0	|	3	 1.00	 0.49	a	a	aaaaa
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	|  0.7 -0.1 -0.1  0.7 -0.1  0.7
c	| -0.0 -0.0 -0.0 -0.0  0.7 -0.0
g	| -0.0 -0.0  0.7 -0.0  0.2 -0.0
t	| -0.1  0.7 -0.0 -0.1 -0.1 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.5  0.5  0.5  0.5  0.7  0.5  3.2
; i.max	|  0.7  0.7  0.7  0.7  0.7  0.7  0.7
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	3
>ems_chr3R_9724360_972437
atgaca
>ems_chr3R_9723844_972385
atgaca
>ems_chr3R_9724540_972455
attaga
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.360|c:0.140|g:0.140|t:0.360
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/ems_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	3
;	meme.llr                     	19
;	meme.E-value                 	17
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.14
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	3.1545
;	information.per.column       	0.52575
;	max.possible.info.per.col    	1.96611
;	consensus.strict             	atGaCa
;	consensus.strict.rc          	tGtCat
;	consensus.IUPAC              	atGaSa
;	consensus.IUPAC.rc           	tStCat
;	consensus.regexp             	atGa[CG]a
;	consensus.regexp.rc          	t[CG]tCat
;	residues.content.crude.freq  	a:0.5000|c:0.1111|g:0.1667|t:0.2222
;	G+C.content.crude.freq       	0.277778
;	residues.content.corrected.freq	a:0.4650|c:0.1183|g:0.1600|t:0.2567
;	G+C.content.corrected.freq   	0.278333
;	min(P(S|M))                  	4.72697e-09
;	max(P(S|M))                  	0.142503
;	proba_range                  	0.142503
;	Wmin                         	-8.4
;	Wmax                         	5.9
;	Wrange                       	14.3
; Job started 2007_12_10.132053
; Job done    2007_12_10.132053