; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/slbo.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/slbo_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/slbo.tab
; Output files
;	output	html_ready/slbo_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : slbo
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	1	2	3	1	0	1	1	10
c	|	4	0	0	0	0	0	10	0
g	|	0	5	5	0	7	10	1	2
t	|	7	5	4	11	5	1	0	0
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	12	12	12	12	12	12	12	12	96
; c.max	|	7	5	5	11	7	10	10	10	11
; c.min	|	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	1	4	0	7	|	12	 0.58	 0.35	t	y	ctt
2	2	0	5	5	|	12	 0.42	 0.28	g	k	g
3	3	0	5	4	|	12	 0.42	 0.23	g	k	g
4	1	0	0	11	|	12	 0.92	 0.69	T	T	TTTTTTTTT
5	0	0	7	5	|	12	 0.58	 0.62	G	K	GGGtt
6	1	0	10	1	|	12	 0.83	 0.87	G	G	GGGGGGGGGGt
7	1	10	1	0	|	12	 0.83	 0.90	C	C	CCCCCCCCCCg
8	10	0	2	0	|	12	 0.83	 0.62	a	a	aaaaaag
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  0.7
c	|  0.2 -0.0 -0.0 -0.0 -0.0 -0.0  1.1 -0.0
g	| -0.0  0.3  0.3 -0.0  0.6  1.1 -0.1 -0.0
t	|  0.3  0.1  0.0  0.9  0.1 -0.1 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.4  0.3  0.2  0.7  0.6  0.9  0.9  0.6  4.6
; i.max	|  0.3  0.3  0.3  0.9  0.6  1.1  1.1  0.7  1.1
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	12
>slbo_chr3L_14044414_1404
tgttggca
>slbo_chr2R_19841710_1984
ctgttgca
>slbo_chr3L_14044547_1404
tagtggca
>slbo_chrX_9898779_989879
tgattgca
>slbo_chr3L_14042599_1404
tttttgca
>slbo_chr3L_14042330_1404
tgtttgcg
>slbo_chr3L_14044503_1404
atttggca
>slbo_chr3L_14042362_1404
ttgtggaa
>slbo_chr3L_14044458_1404
ctgtgtca
>slbo_chr3L_14044316_1404
cgaaggca
>slbo_chrX_9898807_989882
tgattaca
>slbo_chrX_9898854_989886
cagtgggg
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.317|c:0.183|g:0.183|t:0.317
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/slbo_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	12
;	meme.llr                     	68
;	meme.E-value                 	0.14
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.183
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.5554
;	information.per.column       	0.569425
;	max.possible.info.per.col    	1.69827
;	consensus.strict             	tggTGGCa
;	consensus.strict.rc          	tGCCAcca
;	consensus.IUPAC              	ykkTKGCa
;	consensus.IUPAC.rc           	tGCMAmmr
;	consensus.regexp             	[ct][gt][gt]T[GT]GCa
;	consensus.regexp.rc          	tGC[AC]A[ac][ac][ag]
;	residues.content.crude.freq  	a:0.1979|c:0.1458|g:0.3125|t:0.3438
;	G+C.content.crude.freq       	0.458333
;	residues.content.corrected.freq	a:0.2071|c:0.1487|g:0.3025|t:0.3417
;	G+C.content.corrected.freq   	0.451231
;	min(P(S|M))                  	2.67098e-15
;	max(P(S|M))                  	0.0214969
;	proba_range                  	0.0214969
;	Wmin                         	-20.8
;	Wmax                         	8.3
;	Wrange                       	29.1
; Job started 2007_12_10.132125
; Job done    2007_12_10.132125