; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/sna.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/sna_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/sna.tab
; Output files
;	output	html_ready/sna_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : sna
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	5	10	1	1	0	0	1	0
c	|	5	1	10	5	0	1	6	2
g	|	0	0	0	0	0	10	0	2
t	|	1	0	0	5	11	0	4	7
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	11	11	11	11	11	11	11	11	88
; c.max	|	5	10	10	5	11	10	6	7	11
; c.min	|	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	5	5	0	1	|	11	 0.45	 0.35	c	m	ac
2	10	1	0	0	|	11	 0.91	 0.84	A	A	AAAAAAAAAAAcc
3	1	10	0	0	|	11	 0.91	 0.87	C	C	aCCCCCCCCCCCC
4	1	5	0	5	|	11	 0.45	 0.35	c	y	ct
5	0	0	0	11	|	11	 1.00	 1.06	T	T	TTTTTTTTTTTTTTTTTT
6	0	1	10	0	|	11	 0.91	 0.87	G	G	cGGGGGGGGGGGG
7	1	6	0	4	|	11	 0.55	 0.37	c	y	cct
8	0	2	2	7	|	11	 0.64	 0.37	t	t	gtt
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	|  0.2  1.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
c	|  0.3 -0.1  1.1  0.3 -0.1 -0.1  0.4 -0.0
g	| -0.1 -0.1 -0.1 -0.1 -0.1  1.1 -0.1 -0.0
t	| -0.1 -0.1 -0.1  0.2  1.2 -0.1  0.1  0.5
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.3  0.8  0.9  0.3  1.1  0.9  0.4  0.4  5.1
; i.max	|  0.3  1.0  1.1  0.3  1.2  1.1  0.4  0.5  1.2
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	11
>sna_chr3R_8898155_889817
cacttgct
>sna_chr3R_8897880_889791
aacctgtt
>sna_chr3R_8898126_889814
cacctgtt
>sna_chr3L_1445405_144541
aacttgcg
>sna_chr3R_8898032_889807
aacctgcc
>sna_chr3L_1445495_144550
cacttgcg
>sna_chr3R_8895901_889592
cacctgat
>sna_chr3L_1445556_144556
cacatgtt
>sna_chr3R_8896312_889633
tacctgtt
>sna_chr3L_1445475_144548
accttgct
>sna_chr3R_8896062_889607
aaattccc
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.256|c:0.244|g:0.244|t:0.256
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/sna_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	11
;	meme.llr                     	71
;	meme.E-value                 	2.6e-05
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.244
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.07259
;	information.per.column       	0.634073
;	max.possible.info.per.col    	1.41059
;	consensus.strict             	cACcTGct
;	consensus.strict.rc          	agCAgGTg
;	consensus.IUPAC              	mACyTGyt
;	consensus.IUPAC.rc           	arCArGTk
;	consensus.regexp             	[ac]AC[ct]TG[ct]t
;	consensus.regexp.rc          	a[ag]CA[ag]GT[gt]
;	residues.content.crude.freq  	a:0.2045|c:0.3409|g:0.1364|t:0.3182
;	G+C.content.crude.freq       	0.477273
;	residues.content.corrected.freq	a:0.2088|c:0.3328|g:0.1453|t:0.3130
;	G+C.content.corrected.freq   	0.478167
;	min(P(S|M))                  	3.21639e-14
;	max(P(S|M))                  	0.0352632
;	proba_range                  	0.0352632
;	Wmin                         	-20
;	Wmax                         	8.1
;	Wrange                       	28.1
; Job started 2007_12_10.132126
; Job done    2007_12_10.132126