; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ey.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/ey_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ey.tab
; Output files
;	output	html_ready/ey_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : ey
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8	9	10	11
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	8	1	0	0	8	3	1	0	0	0
c	|	8	0	3	0	7	0	1	0	3	0	0
g	|	0	0	2	0	1	0	2	6	1	7	5
t	|	0	0	2	8	0	0	2	1	4	1	3
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	8	8	8	8	8	8	8	8	8	8	8	88
; c.max	|	8	8	3	8	7	8	3	6	4	7	5	8
; c.min	|	0	0	1	0	0	0	1	0	0	0	0	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	0	8	0	0	|	8	 1.00	 1.10	C	C	CCCCCCCCCCCCCCCCC
2	8	0	0	0	|	8	 1.00	 0.93	A	A	AAAAAAAAAAAAAA
3	1	3	2	2	|	8	 0.38	 0.08	c	s	
4	0	0	0	8	|	8	 1.00	 0.93	T	T	TTTTTTTTTTTTTT
5	0	7	1	0	|	8	 0.88	 0.83	C	C	CCCCCCCCCCg
6	8	0	0	0	|	8	 1.00	 0.93	A	A	AAAAAAAAAAAAAA
7	3	1	2	2	|	8	 0.38	 0.03	a	r	
8	1	0	6	1	|	8	 0.75	 0.54	G	G	GGGGGt
9	0	3	1	4	|	8	 0.50	 0.29	t	y	gt
10	0	0	7	1	|	8	 0.88	 0.81	G	G	GGGGGGGGGtt
11	0	0	5	3	|	8	 0.62	 0.53	g	k	gggtt
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8    9   10   11
;-	|-----|----|----|----|----|----|----|----|----|----|----|
a	| -0.1  1.1 -0.1 -0.1 -0.1  1.1  0.1 -0.1 -0.1 -0.1 -0.1
c	|  1.3 -0.1  0.2 -0.1  1.0 -0.1 -0.1 -0.1  0.2 -0.1 -0.1
g	| -0.1 -0.1  0.0 -0.1 -0.1 -0.1  0.0  0.8 -0.1  1.0  0.6
t	| -0.1 -0.1 -0.0  1.1 -0.1 -0.1 -0.0 -0.1  0.3 -0.1  0.1
;-	|-----|----|----|----|----|----|----|----|----|----|----|
; i.sum	|  1.1  0.9  0.1  0.9  0.8  0.9  0.0  0.5  0.3  0.8  0.5  7.0
; i.max	|  1.3  1.1  0.2  1.1  1.0  1.1  0.1  0.8  0.3  1.0  0.6  1.3
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	8
>ey_chr3R_10731653_107316
cagtcaagtgg
>ey_chrX_6613614_6613627_
cactcaagtgt
>ey_chr2R_2943057_2943086
cactcacgtgg
>ey_chr2L_6542972_6542991
caatcaagtgg
>ey_chr2R_3550800_3550819
cattcaggctg
>ey_chr2R_2942930_2942958
cactcattcgt
>ey_chr2R_2943224_2943254
cagtgaggggg
>ey_chrX_6621205_6621224_
cattcatacgt
;
; Matrix parameters
;	Columns                      	11
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.277|c:0.223|g:0.223|t:0.277
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/ey_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	8
;	meme.llr                     	77
;	meme.E-value                 	3.3e-07
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.223
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.9896
;	information.per.column       	0.635419
;	max.possible.info.per.col    	1.50058
;	consensus.strict             	CAcTCAaGtGg
;	consensus.strict.rc          	cCaCtTGAgTG
;	consensus.IUPAC              	CAsTCArGyGk
;	consensus.IUPAC.rc           	mCrCyTGAsTG
;	consensus.regexp             	CA[cg]TCA[ag]G[ct]G[gt]
;	consensus.regexp.rc          	[ac]C[ag]C[ct]TGA[cg]TG
;	residues.content.crude.freq  	a:0.2386|c:0.2500|g:0.2727|t:0.2386
;	G+C.content.crude.freq       	0.522727
;	residues.content.corrected.freq	a:0.2429|c:0.2470|g:0.2672|t:0.2429
;	G+C.content.corrected.freq   	0.514202
;	min(P(S|M))                  	1.04723e-16
;	max(P(S|M))                  	0.0113818
;	proba_range                  	0.0113818
;	Wmin                         	-21
;	Wmax                         	11.1
;	Wrange                       	32.1
; Job started 2007_12_10.132058
; Job done    2007_12_10.132058