; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Abd-B.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Abd-B_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Abd-B.tab
; Output files
;	output	html_ready/Abd-B_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Abd-B
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	3	1	1	6	0	7	7	6
c	|	1	2	5	0	0	0	0	0
g	|	3	0	1	1	0	0	0	0
t	|	0	4	0	0	7	0	0	1
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	7	7	7	7	7	7	7	7	56
; c.max	|	3	4	5	6	7	7	7	6	7
; 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	3	1	3	0	|	7	 0.43	 0.41	G	V	c
2	1	2	0	4	|	7	 0.57	 0.24	c	y	t
3	1	5	1	0	|	7	 0.71	 0.82	C	S	CCCCCg
4	6	0	1	0	|	7	 0.86	 0.49	a	r	aaaa
5	0	0	0	7	|	7	 1.00	 0.67	t	t	ttttttt
6	7	0	0	0	|	7	 1.00	 0.67	a	a	aaaaaaa
7	7	0	0	0	|	7	 1.00	 0.67	a	a	aaaaaaa
8	6	0	0	1	|	7	 0.86	 0.41	a	a	aaat
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	|  0.1 -0.1 -0.1  0.6 -0.1  0.8  0.8  0.6
c	|  0.0  0.2  1.0 -0.0 -0.0 -0.0 -0.0 -0.0
g	|  0.4 -0.0  0.0  0.0 -0.0 -0.0 -0.0 -0.0
t	| -0.1  0.2 -0.1 -0.1  0.8 -0.1 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.4  0.2  0.8  0.5  0.7  0.7  0.7  0.4  4.4
; i.max	|  0.4  0.2  1.0  0.6  0.8  0.8  0.8  0.6  1.0
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	7
>Abd-B_chr3R_9724092_9724
gtcataaa
>Abd-B_chr3R_9724615_9724
gccgtaaa
>Abd-B_chr3R_9723807_9723
ctcataaa
>Abd-B_chr3R_9724558_9724
atcataaa
>Abd-B_chr3R_9724527_9724
atcataaa
>Abd-B_chr3R_9723844_9723
acgataat
>Abd-B_chr3R_9723999_9724
gaaataaa
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.373|c:0.127|g:0.127|t:0.373
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Abd-B_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	7
;	meme.llr                     	44
;	meme.E-value                 	0.0023
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.127
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.37606
;	information.per.column       	0.547007
;	max.possible.info.per.col    	2.06357
;	consensus.strict             	GcCataaa
;	consensus.strict.rc          	tttatGgC
;	consensus.IUPAC              	VySrtaaa
;	consensus.IUPAC.rc           	tttaySrB
;	consensus.regexp             	[ACG][ct][CG][ag]taaa
;	consensus.regexp.rc          	ttta[ct][CG][ag][CGT]
;	residues.content.crude.freq  	a:0.5536|c:0.1429|g:0.0893|t:0.2143
;	G+C.content.crude.freq       	0.232143
;	residues.content.corrected.freq	a:0.5310|c:0.1409|g:0.0940|t:0.2341
;	G+C.content.corrected.freq   	0.234875
;	min(P(S|M))                  	3.47953e-14
;	max(P(S|M))                  	0.073377
;	proba_range                  	0.073377
;	Wmin                         	-16.8
;	Wmax                         	7.8
;	Wrange                       	24.6
; Job started 2007_12_10.132028
; Job done    2007_12_10.132028