; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/vnd.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/vnd_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/vnd.tab
; Output files
;	output	html_ready/vnd_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : vnd
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	0	3	0	0	0	0
c	|	3	0	3	0	0	0
g	|	0	0	0	0	0	3
t	|	0	0	0	3	3	0
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	3	3	3	3	3	3	18
; c.max	|	3	3	3	3	3	3	3
; 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	0	3	0	0	|	3	 1.00	 0.73	C	C	CCCCCCCCCCCC
2	3	0	0	0	|	3	 1.00	 0.66	A	A	AAAAAAAAAA
3	0	3	0	0	|	3	 1.00	 0.73	C	C	CCCCCCCCCCCC
4	0	0	0	3	|	3	 1.00	 0.66	T	T	TTTTTTTTTT
5	0	0	0	3	|	3	 1.00	 0.66	T	T	TTTTTTTTTT
6	0	0	3	0	|	3	 1.00	 0.73	G	G	GGGGGGGGGGGG
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.1  0.9 -0.1 -0.1 -0.1 -0.1
c	|  1.0 -0.1  1.0 -0.1 -0.1 -0.1
g	| -0.1 -0.1 -0.1 -0.1 -0.1  1.0
t	| -0.1 -0.1 -0.1  0.9  0.9 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.7  0.7  0.7  0.7  0.7  0.7  4.2
; i.max	|  1.0  0.9  1.0  0.9  0.9  1.0  1.0
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	3
>vnd_chr3L_15005794_15005
cacttg
>vnd_chr3L_15005821_15005
cacttg
>vnd_chr3L_15005772_15005
cacttg
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.265|c:0.235|g:0.235|t:0.265
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/vnd_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	3
;	meme.llr                     	25
;	meme.E-value                 	0.044
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.235
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.19385
;	information.per.column       	0.698976
;	max.possible.info.per.col    	1.44817
;	consensus.strict             	CACTTG
;	consensus.strict.rc          	CAAGTG
;	consensus.IUPAC              	CACTTG
;	consensus.IUPAC.rc           	CAAGTG
;	consensus.regexp             	CACTTG
;	consensus.regexp.rc          	CAAGTG
;	residues.content.crude.freq  	a:0.1667|c:0.3333|g:0.1667|t:0.3333
;	G+C.content.crude.freq       	0.5
;	residues.content.corrected.freq	a:0.1913|c:0.3088|g:0.1837|t:0.3163
;	G+C.content.corrected.freq   	0.4925
;	min(P(S|M))                  	4.11194e-08
;	max(P(S|M))                  	0.287682
;	proba_range                  	0.287682
;	Wmin                         	-8.4
;	Wmax                         	7
;	Wrange                       	15.4
; Job started 2007_12_10.132139
; Job done    2007_12_10.132139