; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/vvl.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/vvl_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/vvl.tab
; Output files
;	output	html_ready/vvl_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : vvl
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	7	0	1	2	0	5	10	0
c	|	0	2	0	0	0	7	0	0
g	|	4	2	4	0	7	0	0	1
t	|	1	8	7	10	5	0	2	11
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	12	12	12	12	12	12	12	12	96
; c.max	|	7	8	7	10	7	7	10	11	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	7	0	4	1	|	12	 0.58	 0.36	g	r	ag
2	0	2	2	8	|	12	 0.67	 0.35	t	b	gtt
3	1	0	4	7	|	12	 0.58	 0.36	g	k	gt
4	2	0	0	10	|	12	 0.83	 0.47	t	t	ttttt
5	0	0	7	5	|	12	 0.58	 0.69	G	K	GGGtt
6	5	7	0	0	|	12	 0.58	 0.69	C	M	aaCCC
7	10	0	0	2	|	12	 0.83	 0.47	a	a	aaaat
8	0	0	1	11	|	12	 0.92	 0.65	t	t	tttttttt
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	|  0.3 -0.1 -0.1 -0.1 -0.1  0.1  0.7 -0.1
c	| -0.0  0.0 -0.0 -0.0 -0.0  0.7 -0.0 -0.0
g	|  0.2  0.0  0.2 -0.0  0.7 -0.0 -0.0 -0.0
t	| -0.1  0.4  0.3  0.7  0.1 -0.1 -0.1  0.8
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.4  0.4  0.4  0.5  0.7  0.7  0.5  0.7  4.0
; i.max	|  0.3  0.4  0.3  0.7  0.7  0.7  0.7  0.8  0.8
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	12
>vvl_chr3L_14043381_14043
gtgtgcat
>vvl_chr2R_11403677_11403
atttgcat
>vvl_chr3L_6759141_675915
atttgcat
>vvl_chr3L_6758913_675893
gggtgcat
>vvl_chr3L_14044373_14044
ttttgcat
>vvl_chr3L_14043971_14043
atgttaat
>vvl_chr3L_14043358_14043
gttttaat
>vvl_chr2R_8412593_841261
gcatgcat
>vvl_chr3L_14043929_14043
attttaat
>vvl_chr3L_14043906_14043
actttatt
>vvl_chr3L_14044313_14044
atgagctg
>vvl_chr3L_14043830_14043
agtataat
;
; Matrix parameters
;	Columns                      	8
;	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/vvl_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	12
;	meme.llr                     	61
;	meme.E-value                 	4.9
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.149
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.03499
;	information.per.column       	0.504373
;	max.possible.info.per.col    	1.90381
;	consensus.strict             	gtgtGCat
;	consensus.strict.rc          	atGCacac
;	consensus.IUPAC              	rbktKMat
;	consensus.IUPAC.rc           	atKMamvy
;	consensus.regexp             	[ag][cgt][gt]t[GT][AC]at
;	consensus.regexp.rc          	at[GT][AC]a[ac][acg][ct]
;	residues.content.crude.freq  	a:0.2604|c:0.0938|g:0.1875|t:0.4583
;	G+C.content.crude.freq       	0.28125
;	residues.content.corrected.freq	a:0.2674|c:0.0980|g:0.1845|t:0.4501
;	G+C.content.corrected.freq   	0.282538
;	min(P(S|M))                  	7.01559e-16
;	max(P(S|M))                  	0.0343854
;	proba_range                  	0.0343854
;	Wmin                         	-20.8
;	Wmax                         	7.4
;	Wrange                       	28.2
; Job started 2007_12_10.132140
; Job done    2007_12_10.132141