; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/bin.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/bin_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/bin.tab
; Output files
;	output	html_ready/bin_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : bin
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8	9	10
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	0	0	0	0	0	0	1	1	5
c	|	1	5	1	2	0	0	0	0	0	0
g	|	0	0	2	0	0	5	1	0	0	0
t	|	4	0	2	3	5	0	4	4	4	0
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	5	5	5	5	5	5	5	5	5	5	50
; c.max	|	4	5	2	3	5	5	4	4	4	5	5
; c.min	|	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	1	0	4	|	5	 0.80	 0.44	t	y	tttt
2	0	5	0	0	|	5	 1.00	 1.18	C	C	CCCCCCCCCCCCCCC
3	0	1	2	2	|	5	 0.40	 0.27	g	b	t
4	0	2	0	3	|	5	 0.60	 0.41	c	y	ctt
5	0	0	0	5	|	5	 1.00	 0.67	t	t	tttttttt
6	0	0	5	0	|	5	 1.00	 1.18	G	G	GGGGGGGGGGGGGGG
7	0	0	1	4	|	5	 0.80	 0.44	t	k	tttt
8	1	0	0	4	|	5	 0.80	 0.36	t	t	ttt
9	1	0	0	4	|	5	 0.80	 0.36	t	t	ttt
10	5	0	0	0	|	5	 1.00	 0.67	a	a	aaaaaaaa
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8    9   10
;-	|-----|----|----|----|----|----|----|----|----|----|
a	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  0.9
c	|  0.0  1.4  0.0  0.3 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0
g	| -0.0 -0.0  0.3 -0.0 -0.0  1.4  0.0 -0.0 -0.0 -0.0
t	|  0.6 -0.1  0.1  0.3  0.9 -0.1  0.6  0.6  0.6 -0.1
;-	|-----|----|----|----|----|----|----|----|----|----|
; i.sum	|  0.4  1.2  0.3  0.4  0.7  1.2  0.4  0.4  0.4  0.7  6.0
; i.max	|  0.6  1.4  0.3  0.3  0.9  1.4  0.6  0.6  0.6  0.9  1.4
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	5
>bin_chr2L_2445847_244586
tcgctggtta
>bin_chr2R_19816734_19816
tctttgttta
>bin_chr2L_2445777_244580
tccttgttta
>bin_chr2R_19816842_19816
cctttgttta
>bin_chr2L_2446151_244617
tcgctgtaaa
;
; Matrix parameters
;	Columns                      	10
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.336|c:0.164|g:0.164|t:0.336
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/bin_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	5
;	meme.llr                     	48
;	meme.E-value                 	0.53
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.164
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.97911
;	information.per.column       	0.597911
;	max.possible.info.per.col    	1.80789
;	consensus.strict             	tCgctGttta
;	consensus.strict.rc          	taaaCagcGa
;	consensus.IUPAC              	yCbytGktta
;	consensus.IUPAC.rc           	taamCarvGr
;	consensus.regexp             	[ct]C[cgt][ct]tG[gt]tta
;	consensus.regexp.rc          	taa[ac]Ca[ag][acg]G[ag]
;	residues.content.crude.freq  	a:0.1400|c:0.1800|g:0.1600|t:0.5200
;	G+C.content.crude.freq       	0.34
;	residues.content.corrected.freq	a:0.1727|c:0.1773|g:0.1607|t:0.4893
;	G+C.content.corrected.freq   	0.338
;	min(P(S|M))                  	4.76894e-16
;	max(P(S|M))                  	0.0345898
;	proba_range                  	0.0345898
;	Wmin                         	-18
;	Wmax                         	10.3
;	Wrange                       	28.3
; Job started 2007_12_10.132036
; Job done    2007_12_10.132036