; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/br-Z1.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/br-Z1_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/br-Z1.tab
; Output files
;	output	html_ready/br-Z1_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : br-Z1
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7
; -----	|--------|-------|-------|-------|-------|-------|-------|
a	|	0	2	0	0	0	0	0
c	|	0	0	1	2	0	0	0
g	|	2	0	1	0	0	2	2
t	|	0	0	0	0	2	0	0
; -----	|--------|-------|-------|-------|-------|-------|-------|
; c.sum	|	2	2	2	2	2	2	2	14
; c.max	|	2	2	1	2	2	2	2	2
; c.min	|	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	0	2	0	|	2	 1.00	 0.81	G	G	GGGGGGGGGG
2	2	0	0	0	|	2	 1.00	 0.39	a	a	aaaa
3	0	1	1	0	|	2	 0.50	 0.47	c	s	cg
4	0	2	0	0	|	2	 1.00	 0.81	C	C	CCCCCCCCCC
5	0	0	0	2	|	2	 1.00	 0.39	t	t	tttt
6	0	0	2	0	|	2	 1.00	 0.81	G	G	GGGGGGGGGG
7	0	0	2	0	|	2	 1.00	 0.81	G	G	GGGGGGGGGG
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7
;-	|-----|----|----|----|----|----|----|
a	| -0.1  0.6 -0.1 -0.1 -0.1 -0.1 -0.1
c	| -0.1 -0.1  0.4  1.1 -0.1 -0.1 -0.1
g	|  1.1 -0.1  0.4 -0.1 -0.1  1.1  1.1
t	| -0.1 -0.1 -0.1 -0.1  0.6 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|
; i.sum	|  0.8  0.4  0.5  0.8  0.4  0.8  0.8  4.5
; i.max	|  1.1  0.6  0.4  1.1  0.6  1.1  1.1  1.1
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	2
>br-Z1_chr3L_15623023_156
gacctgg
>br-Z1_chrX_3105544_31055
gagctgg
;
; Matrix parameters
;	Columns                      	7
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.351|c:0.149|g:0.149|t:0.351
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/br-Z1_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	2
;	meme.llr                     	22
;	meme.E-value                 	1000
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.149
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.50223
;	information.per.column       	0.643175
;	max.possible.info.per.col    	1.90381
;	consensus.strict             	GacCtGG
;	consensus.strict.rc          	CCaGgtC
;	consensus.IUPAC              	GasCtGG
;	consensus.IUPAC.rc           	CCaGstC
;	consensus.regexp             	Ga[cg]CtGG
;	consensus.regexp.rc          	CCaG[cg]tC
;	residues.content.crude.freq  	a:0.1429|c:0.2143|g:0.5000|t:0.1429
;	G+C.content.crude.freq       	0.714286
;	residues.content.corrected.freq	a:0.2122|c:0.1925|g:0.3830|t:0.2122
;	G+C.content.corrected.freq   	0.575524
;	min(P(S|M))                  	1.75621e-09
;	max(P(S|M))                  	0.061933
;	proba_range                  	0.061933
;	Wmin                         	-7.7
;	Wmax                         	9
;	Wrange                       	16.7
; Job started 2007_12_10.132037
; Job done    2007_12_10.132037