; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Mef2.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Mef2_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Mef2.tab
; Output files
;	output	html_ready/Mef2_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Mef2
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	0	2	0	0	0	0
c	|	0	0	0	1	2	1
g	|	0	0	2	1	0	1
t	|	2	0	0	0	0	0
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	2	2	2	2	2	2	12
; c.max	|	2	2	2	1	2	1	2
; c.min	|	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	0	2	|	2	 1.00	 0.40	t	t	ttttt
2	2	0	0	0	|	2	 1.00	 0.40	a	a	aaaaa
3	0	0	2	0	|	2	 1.00	 0.80	G	G	GGGGGGGGGG
4	0	1	1	0	|	2	 0.50	 0.45	c	s	cg
5	0	2	0	0	|	2	 1.00	 0.80	C	C	CCCCCCCCCC
6	0	1	1	0	|	2	 0.50	 0.45	c	s	cg
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.1  0.6 -0.1 -0.1 -0.1 -0.1
c	| -0.1 -0.1 -0.1  0.4  1.1  0.4
g	| -0.1 -0.1  1.1  0.4 -0.1  0.4
t	|  0.6 -0.1 -0.1 -0.1 -0.1 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.4  0.4  0.8  0.5  0.8  0.5  3.3
; i.max	|  0.6  0.6  1.1  0.4  1.1  0.4  1.1
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	2
>Mef2_chr2R_16451395_1645
taggcg
>Mef2_chr2R_5449608_54496
tagccc
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.346|c:0.154|g:0.154|t:0.346
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Mef2_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	2
;	meme.llr                     	16
;	meme.E-value                 	24
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.154
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	3.28915
;	information.per.column       	0.548192
;	max.possible.info.per.col    	1.8708
;	consensus.strict             	taGcCc
;	consensus.strict.rc          	gGgCta
;	consensus.IUPAC              	taGsCs
;	consensus.IUPAC.rc           	sGsCta
;	consensus.regexp             	taG[cg]C[cg]
;	consensus.regexp.rc          	[cg]G[cg]Cta
;	residues.content.crude.freq  	a:0.1667|c:0.3333|g:0.3333|t:0.1667
;	G+C.content.crude.freq       	0.666667
;	residues.content.corrected.freq	a:0.2264|c:0.2736|g:0.2736|t:0.2264
;	G+C.content.corrected.freq   	0.547111
;	min(P(S|M))                  	9.2365e-08
;	max(P(S|M))                  	0.0466478
;	proba_range                  	0.0466477
;	Wmin                         	-6.6
;	Wmax                         	6.5
;	Wrange                       	13.1
; Job started 2007_12_10.132116
; Job done    2007_12_10.132116