; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/toy.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/toy_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/toy.tab
; Output files
;	output	html_ready/toy_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : toy
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8	9	10	11
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	1	2	1	0	0	5	0	0	0	3
c	|	5	4	2	4	0	5	0	3	1	3	0
g	|	0	0	1	0	0	0	0	0	1	2	2
t	|	0	0	0	0	5	0	0	2	3	0	0
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	5	5	5	5	5	5	5	5	5	5	5	55
; c.max	|	5	4	2	4	5	5	5	3	3	3	3	5
; c.min	|	0	0	0	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	0	5	0	0	|	5	 1.00	 0.95	C	C	CCCCCCCCCCCCCCC
2	1	4	0	0	|	5	 0.80	 0.60	C	C	aCCCCCC
3	2	2	1	0	|	5	 0.40	 0.21	c	m	c
4	1	4	0	0	|	5	 0.80	 0.60	C	C	aCCCCCC
5	0	0	0	5	|	5	 1.00	 0.80	T	T	TTTTTTTTTTTT
6	0	5	0	0	|	5	 1.00	 0.95	C	C	CCCCCCCCCCCCCCC
7	5	0	0	0	|	5	 1.00	 0.80	A	A	AAAAAAAAAAAA
8	0	3	0	2	|	5	 0.60	 0.44	c	y	cctt
9	0	1	1	3	|	5	 0.60	 0.25	t	t	tt
10	0	3	2	0	|	5	 0.60	 0.49	c	s	ccgg
11	3	0	2	0	|	5	 0.60	 0.41	a	r	aag
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8    9   10   11
;-	|-----|----|----|----|----|----|----|----|----|----|----|
a	| -0.1 -0.1  0.1 -0.1 -0.1 -0.1  1.0 -0.1 -0.1 -0.1  0.4
c	|  1.2  0.8  0.2  0.8 -0.1  1.2 -0.1  0.5 -0.0  0.5 -0.1
g	| -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0  0.2  0.2
t	| -0.1 -0.1 -0.1 -0.1  1.0 -0.1 -0.1  0.1  0.4 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|----|----|----|----|
; i.sum	|  1.0  0.6  0.2  0.6  0.8  1.0  0.8  0.4  0.3  0.5  0.4  6.5
; i.max	|  1.2  0.8  0.2  0.8  1.0  1.2  1.0  0.5  0.4  0.5  0.4  1.2
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	5
>toy_chr2R_2943224_294325
cccctcactgg
>toy_chr2R_2942930_294295
ccactcattcg
>toy_chr2R_2943105_294312
cccctcaccga
>toy_chr2R_2943057_294308
caactcactca
>toy_chr2R_2943142_294316
ccgatcatgca
;
; Matrix parameters
;	Columns                      	11
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.277|c:0.223|g:0.223|t:0.277
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/toy_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	5
;	meme.llr                     	53
;	meme.E-value                 	0.39
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.223
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.51942
;	information.per.column       	0.592675
;	max.possible.info.per.col    	1.50058
;	consensus.strict             	CCcCTCActca
;	consensus.strict.rc          	tgagTGAGgGG
;	consensus.IUPAC              	CCmCTCAytsr
;	consensus.IUPAC.rc           	ysarTGAGkGG
;	consensus.regexp             	CC[ac]CTCA[ct]t[cg][ag]
;	consensus.regexp.rc          	[ct][cg]a[ag]TGAG[gt]GG
;	residues.content.crude.freq  	a:0.2182|c:0.4909|g:0.1091|t:0.1818
;	G+C.content.crude.freq       	0.6
;	residues.content.corrected.freq	a:0.2280|c:0.4463|g:0.1281|t:0.1977
;	G+C.content.corrected.freq   	0.574333
;	min(P(S|M))                  	3.58273e-16
;	max(P(S|M))                  	0.00948482
;	proba_range                  	0.00948482
;	Wmin                         	-19.8
;	Wmax                         	11.2
;	Wrange                       	31
; Job started 2007_12_10.132134
; Job done    2007_12_10.132134