; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/exd.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/exd_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/exd.tab
; Output files
;	output	html_ready/exd_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : exd
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	6	1	0	3	6	3
c	|	0	0	5	0	0	0
g	|	0	2	0	2	0	0
t	|	0	3	1	1	0	3
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	6	6	6	6	6	6	36
; c.max	|	6	3	5	3	6	3	6
; 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	6	0	0	0	|	6	 1.00	 0.68	a	a	aaaaaaaa
2	1	0	2	3	|	6	 0.50	 0.21	g	k	t
3	0	5	0	1	|	6	 0.83	 0.92	C	C	CCCCCCCCt
4	3	0	2	1	|	6	 0.50	 0.21	g	r	g
5	6	0	0	0	|	6	 1.00	 0.68	a	a	aaaaaaaa
6	3	0	0	3	|	6	 0.50	 0.21	a	w	t
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	|  0.9 -0.1 -0.1  0.1  0.9  0.1
c	| -0.0 -0.0  1.2 -0.0 -0.0 -0.0
g	| -0.0  0.2 -0.0  0.2 -0.0 -0.0
t	| -0.1  0.1 -0.1 -0.1 -0.1  0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.7  0.2  0.9  0.2  0.7  0.2  2.9
; i.max	|  0.9  0.2  1.2  0.2  0.9  0.1  1.2
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1
; Sites	6
>exd_chr2L_2446086_244609
atcgaa
>exd_chr2L_2446334_244634
atcgat
>exd_chr2L_2446190_244619
atcaat
>exd_chr3R_2613153_261317
agctaa
>exd_chr2L_2446120_244613
aacaaa
>exd_chr2L_2446266_244627
agtaat
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.351|c:0.149|g:0.149|t:0.351
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/exd_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	6
;	meme.llr                     	26
;	meme.E-value                 	96
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.149
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	2.92401
;	information.per.column       	0.487335
;	max.possible.info.per.col    	1.90381
;	consensus.strict             	agCgaa
;	consensus.strict.rc          	ttcGct
;	consensus.IUPAC              	akCraw
;	consensus.IUPAC.rc           	wtyGmt
;	consensus.regexp             	a[gt]C[ag]a[at]
;	consensus.regexp.rc          	[at]t[ct]G[ac]t
;	residues.content.crude.freq  	a:0.5278|c:0.1389|g:0.1111|t:0.2222
;	G+C.content.crude.freq       	0.25
;	residues.content.corrected.freq	a:0.5025|c:0.1403|g:0.1165|t:0.2406
;	G+C.content.corrected.freq   	0.256857
;	min(P(S|M))                  	9.30099e-11
;	max(P(S|M))                  	0.0664266
;	proba_range                  	0.0664266
;	Wmin                         	-11.4
;	Wmax                         	5.2
;	Wrange                       	16.6
; Job started 2007_12_10.132057
; Job done    2007_12_10.132057