; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/grh.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/grh_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/grh.tab
; Output files
;	output	html_ready/grh_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : grh
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	5	5	5	5	1	0	5	0
c	|	0	0	0	0	4	5	0	0
g	|	0	0	0	0	0	0	0	4
t	|	0	0	0	0	0	0	0	1
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	5	5	5	5	5	5	5	5	40
; c.max	|	5	5	5	5	4	5	5	4	5
; c.min	|	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	5	0	0	0	|	5	 1.00	 0.82	A	A	AAAAAAAAAAAAA
2	5	0	0	0	|	5	 1.00	 0.82	A	A	AAAAAAAAAAAAA
3	5	0	0	0	|	5	 1.00	 0.82	A	A	AAAAAAAAAAAAA
4	5	0	0	0	|	5	 1.00	 0.82	A	A	AAAAAAAAAAAAA
5	1	4	0	0	|	5	 0.80	 0.58	C	C	aCCCCCC
6	0	5	0	0	|	5	 1.00	 0.93	C	C	CCCCCCCCCCCCCCC
7	5	0	0	0	|	5	 1.00	 0.82	A	A	AAAAAAAAAAAAA
8	0	0	4	1	|	5	 0.80	 0.58	G	G	GGGGGGt
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	|  1.0  1.0  1.0  1.0 -0.1 -0.1  1.0 -0.1
c	| -0.1 -0.1 -0.1 -0.1  0.8  1.2 -0.1 -0.1
g	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  0.8
t	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.8  0.8  0.8  0.8  0.6  0.9  0.8  0.6  6.2
; i.max	|  1.0  1.0  1.0  1.0  0.8  1.2  1.0  0.8  1.2
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	5
>grh_chr3R_2688374_268838
aaaaccag
>grh_chr2R_15777573_15777
aaaaccag
>grh_chr3R_12560254_12560
aaaaccag
>grh_chr3R_2688329_268836
aaaaccat
>grh_chr3R_2688282_268829
aaaaacag
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.268|c:0.232|g:0.232|t:0.268
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/grh_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	5
;	meme.llr                     	50
;	meme.E-value                 	0.28
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.232
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.21123
;	information.per.column       	0.776403
;	max.possible.info.per.col    	1.46102
;	consensus.strict             	AAAACCAG
;	consensus.strict.rc          	CTGGTTTT
;	consensus.IUPAC              	AAAACCAG
;	consensus.IUPAC.rc           	CTGGTTTT
;	consensus.regexp             	AAAACCAG
;	consensus.regexp.rc          	CTGGTTTT
;	residues.content.crude.freq  	a:0.6500|c:0.2250|g:0.1000|t:0.0250
;	G+C.content.crude.freq       	0.325
;	residues.content.corrected.freq	a:0.5863|c:0.2262|g:0.1220|t:0.0655
;	G+C.content.corrected.freq   	0.348167
;	min(P(S|M))                  	4.99682e-12
;	max(P(S|M))                  	0.226349
;	proba_range                  	0.226349
;	Wmin                         	-14.4
;	Wmax                         	9.6
;	Wrange                       	24
; Job started 2007_12_10.132104
; Job done    2007_12_10.132104