; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Hr46.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Hr46_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Hr46.tab
; Output files
;	output	html_ready/Hr46_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Hr46
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	0	0	0	0	0	0
c	|	0	0	0	0	0	2
g	|	0	3	3	3	0	0
t	|	3	0	0	0	3	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	0	3	|	3	 1.00	 0.59	T	T	TTTTTTTT
2	0	0	3	0	|	3	 1.00	 0.83	G	G	GGGGGGGGGGGG
3	0	0	3	0	|	3	 1.00	 0.83	G	G	GGGGGGGGGGGG
4	0	0	3	0	|	3	 1.00	 0.83	G	G	GGGGGGGGGGGG
5	0	0	0	3	|	3	 1.00	 0.59	T	T	TTTTTTTT
6	0	2	0	1	|	3	 0.67	 0.41	C	Y	CCtt
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
c	| -0.1 -0.1 -0.1 -0.1 -0.1  0.6
g	| -0.1  1.1  1.1  1.1 -0.1 -0.1
t	|  0.8 -0.1 -0.1 -0.1  0.8  0.0
;-	|-----|----|----|----|----|----|
; i.sum	|  0.6  0.8  0.8  0.8  0.6  0.4  4.1
; i.max	|  0.8  1.1  1.1  1.1  0.8  0.6  1.1
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	3
>Hr46_chr3L_18730825_1873
tgggtc
>Hr46_chr3L_18730543_1873
tgggtc
>Hr46_chr3L_18730713_1873
tgggtt
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.300|c:0.200|g:0.200|t:0.300
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Hr46_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	3
;	meme.llr                     	24
;	meme.E-value                 	3.9
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.2
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.08838
;	information.per.column       	0.681396
;	max.possible.info.per.col    	1.60944
;	consensus.strict             	TGGGTC
;	consensus.strict.rc          	GACCCA
;	consensus.IUPAC              	TGGGTY
;	consensus.IUPAC.rc           	RACCCA
;	consensus.regexp             	TGGGT[CT]
;	consensus.regexp.rc          	[AG]ACCCA
;	residues.content.crude.freq  	a:0.0000|c:0.1111|g:0.5000|t:0.3889
;	G+C.content.crude.freq       	0.611111
;	residues.content.corrected.freq	a:0.0750|c:0.1333|g:0.4250|t:0.3667
;	G+C.content.corrected.freq   	0.558333
;	min(P(S|M))                  	1.5625e-08
;	max(P(S|M))                  	0.191664
;	proba_range                  	0.191664
;	Wmin                         	-8.4
;	Wmax                         	7.3
;	Wrange                       	15.7
; Job started 2007_12_10.132109
; Job done    2007_12_10.132109