; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/gt.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/gt_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/gt.tab
; Output files
;	output	html_ready/gt_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : gt
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8	9	10
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
a	|	3	0	5	0	0	6	0	0	0	5
c	|	0	0	0	0	0	2	5	0	3	0
g	|	0	1	2	0	5	0	2	4	0	0
t	|	5	7	1	8	3	0	1	4	5	3
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	8	8	8	8	8	8	8	8	8	8	80
; c.max	|	5	7	5	8	5	6	5	4	5	5	8
; c.min	|	0	0	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	3	0	0	5	|	8	 0.62	 0.29	t	w	tt
2	0	0	1	7	|	8	 0.88	 0.57	t	t	tttttt
3	5	0	2	1	|	8	 0.62	 0.27	a	r	at
4	0	0	0	8	|	8	 1.00	 0.78	T	T	TTTTTTTTTT
5	0	0	5	3	|	8	 0.62	 0.63	G	K	GGGtt
6	6	2	0	0	|	8	 0.75	 0.49	a	m	aaac
7	0	5	2	1	|	8	 0.62	 0.61	C	S	CCCgt
8	0	0	4	4	|	8	 0.50	 0.53	G	K	Gtt
9	0	3	0	5	|	8	 0.62	 0.48	c	y	cttt
10	5	0	0	3	|	8	 0.62	 0.29	a	w	at
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8    9   10
;-	|-----|----|----|----|----|----|----|----|----|----|
a	|  0.0 -0.1  0.3 -0.1 -0.1  0.5 -0.1 -0.1 -0.1  0.3
c	| -0.0 -0.0 -0.0 -0.0 -0.0  0.1  0.7 -0.0  0.3 -0.0
g	| -0.0 -0.0  0.1 -0.0  0.7 -0.0  0.1  0.5 -0.0 -0.0
t	|  0.3  0.7 -0.1  0.9  0.0 -0.1 -0.1  0.2  0.3  0.0
;-	|-----|----|----|----|----|----|----|----|----|----|
; i.sum	|  0.3  0.6  0.3  0.8  0.6  0.5  0.6  0.5  0.5  0.3  4.9
; i.max	|  0.3  0.7  0.3  0.9  0.7  0.5  0.7  0.5  0.3  0.3  0.9
; i.min	| -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1
; Sites	8
>gt_chr2R_20730906_207309
ttatgacgca
>gt_chr2R_5490014_5490036
ttatgacttt
>gt_chr3R_12636939_126369
atattacgta
>gt_chr2R_20732895_207329
atgttacgta
>gt_chr2R_5489682_5489707
ttattagtca
>gt_chr3L_20630776_206307
ttgtgcgttt
>gt_chr3L_20630799_206308
ttttgacttt
>gt_chr2R_5489745_5489789
agatgctgca
;
; Matrix parameters
;	Columns                      	10
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.336|c:0.164|g:0.164|t:0.336
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/gt_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	8
;	meme.llr                     	56
;	meme.E-value                 	11
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.164
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.94506
;	information.per.column       	0.494506
;	max.possible.info.per.col    	1.80789
;	consensus.strict             	ttaTGaCGca
;	consensus.strict.rc          	tgCGtCAtaa
;	consensus.IUPAC              	wtrTKmSKyw
;	consensus.IUPAC.rc           	wrMSkMAyaw
;	consensus.regexp             	[at]t[ag]T[GT][ac][CG][GT][ct][at]
;	consensus.regexp.rc          	[at][ag][AC][CG][gt][AC]A[ct]a[at]
;	residues.content.crude.freq  	a:0.2375|c:0.1250|g:0.1750|t:0.4625
;	G+C.content.crude.freq       	0.3
;	residues.content.corrected.freq	a:0.2484|c:0.1293|g:0.1738|t:0.4484
;	G+C.content.corrected.freq   	0.303111
;	min(P(S|M))                  	8.27006e-18
;	max(P(S|M))                  	0.0104167
;	proba_range                  	0.0104167
;	Wmin                         	-22
;	Wmax                         	8.9
;	Wrange                       	30.9
; Job started 2007_12_10.132105
; Job done    2007_12_10.132105