; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/gl.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/gl_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/gl.tab
; Output files
;	output	html_ready/gl_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : gl
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8	9	10	11
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
a	|	5	0	0	0	1	4	3	0	1	3	0
c	|	0	0	0	0	2	1	0	0	1	0	0
g	|	0	1	0	1	2	0	0	4	2	2	0
t	|	0	4	5	4	0	0	2	1	1	0	5
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	5	5	5	5	5	5	5	5	5	5	5	55
; c.max	|	5	4	5	4	2	4	3	4	2	3	5	5
; c.min	|	0	0	0	0	0	0	0	0	1	0	0	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	5	0	0	0	|	5	 1.00	 0.74	A	A	AAAAAAAAAA
2	0	0	1	4	|	5	 0.80	 0.47	t	k	gtttt
3	0	0	0	5	|	5	 1.00	 0.74	T	T	TTTTTTTTTT
4	0	0	1	4	|	5	 0.80	 0.47	t	k	gtttt
5	1	2	2	0	|	5	 0.40	 0.29	c	s	c
6	4	1	0	0	|	5	 0.80	 0.47	a	m	aaaac
7	3	0	0	2	|	5	 0.60	 0.30	a	w	at
8	0	0	4	1	|	5	 0.80	 0.66	G	G	GGGGGGt
9	1	1	2	1	|	5	 0.40	 0.08	g	s	
10	3	0	2	0	|	5	 0.60	 0.41	g	r	aag
11	0	0	0	5	|	5	 1.00	 0.74	T	T	TTTTTTTTTT
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8    9   10   11
;-	|-----|----|----|----|----|----|----|----|----|----|----|
a	|  0.9 -0.1 -0.1 -0.1 -0.1  0.6  0.3 -0.1 -0.1  0.3 -0.1
c	| -0.1 -0.1 -0.1 -0.1  0.2  0.0 -0.1 -0.1  0.0 -0.1 -0.1
g	| -0.1  0.0 -0.1  0.0  0.2 -0.1 -0.1  0.9  0.2  0.2 -0.1
t	| -0.1  0.6  0.9  0.6 -0.1 -0.1  0.1 -0.1 -0.1 -0.1  0.9
;-	|-----|----|----|----|----|----|----|----|----|----|----|
; i.sum	|  0.7  0.5  0.7  0.5  0.3  0.5  0.3  0.7  0.1  0.4  0.7  5.4
; i.max	|  0.9  0.6  0.9  0.6  0.2  0.6  0.3  0.9  0.2  0.3  0.9  0.9
; 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	5
>gl_chr3R_15714115_157141
atttcaagggt
>gl_chr3R_15714233_157142
atttgaagaat
>gl_chr3R_14200860_142009
atttcattgat
>gl_chr3R_15714205_157142
atttaatgtgt
>gl_chr3R_14200938_142009
agtggcagcat
;
; Matrix parameters
;	Columns                      	11
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.303|c:0.197|g:0.197|t:0.303
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/gl_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	5
;	meme.llr                     	44
;	meme.E-value                 	110
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.197
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.37628
;	information.per.column       	0.488753
;	max.possible.info.per.col    	1.62455
;	consensus.strict             	AtTtcaaGggT
;	consensus.strict.rc          	AccCttgaAaT
;	consensus.IUPAC              	AkTksmwGsrT
;	consensus.IUPAC.rc           	AysCwksmAmT
;	consensus.regexp             	A[gt]T[gt][cg][ac][at]G[cg][ag]T
;	consensus.regexp.rc          	A[ct][cg]C[at][gt][cg][ac]A[ac]T
;	residues.content.crude.freq  	a:0.3091|c:0.0727|g:0.2182|t:0.4000
;	G+C.content.crude.freq       	0.290909
;	residues.content.corrected.freq	a:0.3081|c:0.0934|g:0.2147|t:0.3838
;	G+C.content.corrected.freq   	0.308091
;	min(P(S|M))                  	4.46755e-16
;	max(P(S|M))                  	0.00723821
;	proba_range                  	0.00723821
;	Wmin                         	-18.3
;	Wmax                         	9.8
;	Wrange                       	28.1
; Job started 2007_12_10.132103
; Job done    2007_12_10.132103