; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/zen.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/zen_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/zen.tab
; Output files
;	output	html_ready/zen_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : zen
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	9	0	2	12	9	2	0	5
c	|	1	0	2	0	0	4	4	5
g	|	0	0	0	0	3	0	8	1
t	|	2	12	8	0	0	6	0	1
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	12	12	12	12	12	12	12	12	96
; c.max	|	9	12	8	12	9	6	8	5	12
; c.min	|	0	0	0	0	0	0	0	1	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	9	1	0	2	|	12	 0.75	 0.27	a	a	at
2	0	0	0	12	|	12	 1.00	 0.74	t	t	tttttttt
3	2	2	0	8	|	12	 0.67	 0.23	t	y	t
4	12	0	0	0	|	12	 1.00	 0.74	a	a	aaaaaaaa
5	9	0	3	0	|	12	 0.75	 0.53	g	r	aaag
6	2	4	0	6	|	12	 0.50	 0.28	C	Y	t
7	0	4	8	0	|	12	 0.67	 1.22	G	S	CCCGGGGGG
8	5	5	1	1	|	12	 0.42	 0.35	C	M	C
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	|  0.5 -0.1 -0.1  0.9  0.5 -0.1 -0.1  0.0
c	| -0.0 -0.0  0.1 -0.0 -0.0  0.3  0.3  0.5
g	| -0.0 -0.0 -0.0 -0.0  0.2 -0.0  1.1 -0.0
t	| -0.1  0.9  0.3 -0.1 -0.1  0.1 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.3  0.7  0.2  0.7  0.5  0.3  1.2  0.4  4.4
; i.max	|  0.5  0.9  0.3  0.9  0.5  0.3  1.1  0.5  1.1
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	12
>zen_chr2R_15777851_15777
attaacgc
>zen_chr3R_12560060_12560
atcagcgg
>zen_chr3R_12559847_12559
attagcca
>zen_chr2R_15777955_15777
attaaagc
>zen_chr2R_7044643_704466
attaacca
>zen_chr2L_13905029_13905
ataagtgc
>zen_chr2L_13905145_13905
attaatga
>zen_chr2L_13905234_13905
tttaatgc
>zen_chr3R_17497594_17497
cttaatcc
>zen_chr2R_7044683_704471
atcaatca
>zen_chr2R_15777994_15778
attaaagt
>zen_chr2R_7044520_704454
ttaaatga
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.385|c:0.115|g:0.115|t:0.385
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/zen_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	12
;	meme.llr                     	66
;	meme.E-value                 	1300
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.115
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.37361
;	information.per.column       	0.546701
;	max.possible.info.per.col    	2.16282
;	consensus.strict             	attagCGC
;	consensus.strict.rc          	GCGctaat
;	consensus.IUPAC              	atyarYSM
;	consensus.IUPAC.rc           	KSRytrat
;	consensus.regexp             	at[ct]a[ag][CT][CG][AC]
;	consensus.regexp.rc          	[GT][CG][AG][ct]t[ag]at
;	residues.content.crude.freq  	a:0.4062|c:0.1667|g:0.1250|t:0.3021
;	G+C.content.crude.freq       	0.291667
;	residues.content.corrected.freq	a:0.4046|c:0.1627|g:0.1242|t:0.3085
;	G+C.content.corrected.freq   	0.286923
;	min(P(S|M))                  	1.21724e-15
;	max(P(S|M))                  	0.0387482
;	proba_range                  	0.0387482
;	Wmin                         	-19.5
;	Wmax                         	7.6
;	Wrange                       	27.1
; Job started 2007_12_10.132143
; Job done    2007_12_10.132143