; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ovo.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/ovo_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ovo.tab
; Output files
;	output	html_ready/ovo_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : ovo
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7
; -----	|--------|-------|-------|-------|-------|-------|-------|
a	|	0	3	0	0	0	11	2
c	|	12	6	0	1	0	0	7
g	|	0	0	12	0	0	1	1
t	|	0	3	0	11	12	0	2
; -----	|--------|-------|-------|-------|-------|-------|-------|
; c.sum	|	12	12	12	12	12	12	12	84
; c.max	|	12	6	12	11	12	11	7	12
; c.min	|	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	0	12	0	0	|	12	 1.00	 1.38	C	C	CCCCCCCCCCCCCCCCCCC
2	3	6	0	3	|	12	 0.50	 0.31	c	c	ct
3	0	0	12	0	|	12	 1.00	 1.38	G	G	GGGGGGGGGGGGGGGGGGG
4	0	1	0	11	|	12	 0.92	 0.71	T	T	TTTTTTTTT
5	0	0	0	12	|	12	 1.00	 0.90	T	T	TTTTTTTTTTTT
6	11	0	1	0	|	12	 0.92	 0.71	A	A	AAAAAAAAg
7	2	7	1	2	|	12	 0.58	 0.35	C	C	CC
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7
;-	|-----|----|----|----|----|----|----|
a	| -0.1 -0.1 -0.1 -0.1 -0.1  0.9 -0.1
c	|  1.5  0.5 -0.0 -0.1 -0.0 -0.0  0.6
g	| -0.0 -0.0  1.5 -0.0 -0.0 -0.1 -0.1
t	| -0.1 -0.1 -0.1  0.9  1.0 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|
; i.sum	|  1.4  0.3  1.4  0.7  0.9  0.7  0.3  5.7
; i.max	|  1.5  0.5  1.5  0.9  1.0  0.9  0.6  1.5
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	12
>ovo_chrX_8334701_8334725
ccgttac
>ovo_chr3R_19106286_19106
ccgttac
>ovo_chrX_4908876_4908894
ctgttac
>ovo_chrX_6937188_6937207
ctgttac
>ovo_chrX_4909463_4909485
cagttac
>ovo_chrX_4909224_4909246
cagttac
>ovo_chrX_6937587_6937607
ccgttaa
>ovo_chrX_4909155_4909183
ccgttaa
>ovo_chrX_4909550_4909568
ccgttgc
>ovo_chrX_8334977_8335001
ctgttat
>ovo_chrX_4909379_4909403
cagttag
>ovo_chrX_8335007_8335031
ccgctat
;
; Matrix parameters
;	Columns                      	7
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.319|c:0.181|g:0.181|t:0.319
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/ovo_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	12
;	meme.llr                     	86
;	meme.E-value                 	5.6e-08
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.181
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.73744
;	information.per.column       	0.819634
;	max.possible.info.per.col    	1.70926
;	consensus.strict             	CcGTTAC
;	consensus.strict.rc          	GTAACgG
;	consensus.IUPAC              	CcGTTAC
;	consensus.IUPAC.rc           	GTAACgG
;	consensus.regexp             	CcGTTAC
;	consensus.regexp.rc          	GTAACgG
;	residues.content.crude.freq  	a:0.1905|c:0.3095|g:0.1667|t:0.3333
;	G+C.content.crude.freq       	0.47619
;	residues.content.corrected.freq	a:0.2004|c:0.2996|g:0.1678|t:0.3322
;	G+C.content.corrected.freq   	0.467407
;	min(P(S|M))                  	6.61786e-13
;	max(P(S|M))                  	0.165652
;	proba_range                  	0.165652
;	Wmin                         	-16.3
;	Wmax                         	8.5
;	Wrange                       	24.8
; Job started 2007_12_10.132118
; Job done    2007_12_10.132118