; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/p120.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/p120_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/p120.tab
; Output files
;	output	html_ready/p120_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : p120
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	0	0	1	0	0	2
c	|	0	2	0	1	2	0
g	|	2	0	1	1	0	0
t	|	0	0	0	0	0	0
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	2	2	2	2	2	2	12
; c.max	|	2	2	1	1	2	2	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	2	0	|	2	 1.00	 0.85	G	G	GGGGGGGGGG
2	0	2	0	0	|	2	 1.00	 0.85	C	C	CCCCCCCCCC
3	1	0	1	0	|	2	 0.50	 0.30	g	r	g
4	0	1	1	0	|	2	 0.50	 0.50	c	s	cgg
5	0	2	0	0	|	2	 1.00	 0.85	C	C	CCCCCCCCCC
6	2	0	0	0	|	2	 1.00	 0.38	a	a	aaaa
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.1 -0.1  0.1 -0.1 -0.1  0.6
c	| -0.1  1.2 -0.1  0.4  1.2 -0.1
g	|  1.2 -0.1  0.4  0.4 -0.1 -0.1
t	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.8  0.8  0.3  0.5  0.8  0.4  3.7
; i.max	|  1.2  1.2  0.4  0.4  1.2  0.6  1.2
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	2
>p120_chr3L_8700197_87002
gcgcca
>p120_chr3L_8700293_87003
gcagca
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.360|c:0.140|g:0.140|t:0.360
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/p120_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	2
;	meme.llr                     	18
;	meme.E-value                 	56
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.14
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	3.71639
;	information.per.column       	0.619399
;	max.possible.info.per.col    	1.96611
;	consensus.strict             	GCgcCa
;	consensus.strict.rc          	tGgcGC
;	consensus.IUPAC              	GCrsCa
;	consensus.IUPAC.rc           	tGsyGC
;	consensus.regexp             	GC[ag][cg]Ca
;	consensus.regexp.rc          	tG[cg][ct]GC
;	residues.content.crude.freq  	a:0.2500|c:0.4167|g:0.3333|t:0.0000
;	G+C.content.crude.freq       	0.75
;	residues.content.corrected.freq	a:0.2867|c:0.3244|g:0.2689|t:0.1200
;	G+C.content.corrected.freq   	0.593333
;	min(P(S|M))                  	2.65592e-08
;	max(P(S|M))                  	0.0491892
;	proba_range                  	0.0491892
;	Wmin                         	-6.6
;	Wmax                         	7.7
;	Wrange                       	14.3
; Job started 2007_12_10.132119
; Job done    2007_12_10.132119