; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Cf2-II.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Cf2-II_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Cf2-II.tab
; Output files
;	output	html_ready/Cf2-II_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Cf2-II
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	0	0	3	0	3	2
c	|	0	0	0	0	0	0
g	|	3	0	0	0	0	0
t	|	0	3	0	3	0	1
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	3	3	3	3	3	3	18
; c.max	|	3	3	3	3	3	2	3
; 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	3	0	|	3	 1.00	 0.98	G	G	GGGGGGGGGGGG
2	0	0	0	3	|	3	 1.00	 0.52	t	t	tttttt
3	3	0	0	0	|	3	 1.00	 0.52	a	a	aaaaaa
4	0	0	0	3	|	3	 1.00	 0.52	t	t	tttttt
5	3	0	0	0	|	3	 1.00	 0.52	a	a	aaaaaa
6	2	0	0	1	|	3	 0.67	 0.20	a	a	a
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.1 -0.1  0.7 -0.1  0.7  0.3
c	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
g	|  1.3 -0.1 -0.1 -0.1 -0.1 -0.1
t	| -0.1  0.7 -0.1  0.7 -0.1 -0.0
;-	|-----|----|----|----|----|----|
; i.sum	|  1.0  0.5  0.5  0.5  0.5  0.2  3.2
; i.max	|  1.3  0.7  0.7  0.7  0.7  0.3  1.3
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	3
>Cf2-II_chr3L_8702392_870
gtataa
>Cf2-II_chr2L_4883210_488
gtataa
>Cf2-II_chr3L_8702357_870
gtatat
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.343|c:0.157|g:0.157|t:0.343
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Cf2-II_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	3
;	meme.llr                     	20
;	meme.E-value                 	52
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.157
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	3.2463
;	information.per.column       	0.54105
;	max.possible.info.per.col    	1.85151
;	consensus.strict             	Gtataa
;	consensus.strict.rc          	ttataC
;	consensus.IUPAC              	Gtataa
;	consensus.IUPAC.rc           	ttataC
;	consensus.regexp             	Gtataa
;	consensus.regexp.rc          	ttataC
;	residues.content.crude.freq  	a:0.4444|c:0.0000|g:0.1667|t:0.3889
;	G+C.content.crude.freq       	0.166667
;	residues.content.corrected.freq	a:0.4191|c:0.0393|g:0.1643|t:0.3774
;	G+C.content.corrected.freq   	0.2035
;	min(P(S|M))                  	3.65627e-09
;	max(P(S|M))                  	0.225545
;	proba_range                  	0.225545
;	Wmin                         	-8.4
;	Wmax                         	5.8
;	Wrange                       	14.2
; Job started 2007_12_10.132044
; Job done    2007_12_10.132044