; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/dsx-M.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/dsx-M_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/dsx-M.tab
; Output files
;	output	html_ready/dsx-M_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : dsx-M
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8	9
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	0	2	0	2	3	2	0	0
c	|	3	0	0	3	0	0	0	0	0
g	|	0	0	1	0	0	0	0	3	0
t	|	0	3	0	0	1	0	1	0	3
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	3	3	3	3	3	3	3	3	3	27
; c.max	|	3	3	2	3	2	3	2	3	3	3
; c.min	|	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	3	0	0	|	3	 1.00	 0.91	C	C	CCCCCCCCCCCC
2	0	0	0	3	|	3	 1.00	 0.55	t	t	ttttttt
3	2	0	1	0	|	3	 0.67	 0.32	a	r	ag
4	0	3	0	0	|	3	 1.00	 0.91	C	C	CCCCCCCCCCCC
5	2	0	0	1	|	3	 0.67	 0.22	a	w	at
6	3	0	0	0	|	3	 1.00	 0.55	a	a	aaaaaaa
7	2	0	0	1	|	3	 0.67	 0.22	a	w	at
8	0	0	3	0	|	3	 1.00	 0.91	G	G	GGGGGGGGGGGG
9	0	0	0	3	|	3	 1.00	 0.55	t	t	ttttttt
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8    9
;-	|-----|----|----|----|----|----|----|----|----|
a	| -0.1 -0.1  0.3 -0.1  0.3  0.8  0.3 -0.1 -0.1
c	|  1.2 -0.1 -0.1  1.2 -0.1 -0.1 -0.1 -0.1 -0.1
g	| -0.1 -0.1  0.2 -0.1 -0.1 -0.1 -0.1  1.2 -0.1
t	| -0.1  0.8 -0.1 -0.1  0.0 -0.1  0.0 -0.1  0.8
;-	|-----|----|----|----|----|----|----|----|----|
; i.sum	|  0.9  0.5  0.3  0.9  0.2  0.5  0.2  0.9  0.5  5.1
; i.max	|  1.2  0.8  0.3  1.2  0.3  0.8  0.3  1.2  0.8  1.2
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	3
>dsx-M_chrX_9898797_98988
ctacaaagt
>dsx-M_chrX_9898773_98987
ctacaatgt
>dsx-M_chrX_9898841_98988
ctgctaagt
;
; Matrix parameters
;	Columns                      	9
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.324|c:0.176|g:0.176|t:0.324
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/dsx-M_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	3
;	meme.llr                     	31
;	meme.E-value                 	6.6
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.176
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.14291
;	information.per.column       	0.571435
;	max.possible.info.per.col    	1.73727
;	consensus.strict             	CtaCaaaGt
;	consensus.strict.rc          	aCtttGtaG
;	consensus.IUPAC              	CtrCwawGt
;	consensus.IUPAC.rc           	aCwtwGyaG
;	consensus.regexp             	Ct[ag]C[at]a[at]Gt
;	consensus.regexp.rc          	aC[at]t[at]G[ct]aG
;	residues.content.crude.freq  	a:0.3333|c:0.2222|g:0.1481|t:0.2963
;	G+C.content.crude.freq       	0.37037
;	residues.content.corrected.freq	a:0.3310|c:0.2107|g:0.1551|t:0.3032
;	G+C.content.corrected.freq   	0.365778
;	min(P(S|M))                  	6.18122e-13
;	max(P(S|M))                  	0.0563369
;	proba_range                  	0.0563369
;	Wmin                         	-12.6
;	Wmax                         	9.1
;	Wrange                       	21.7
; Job started 2007_12_10.132051
; Job done    2007_12_10.132051