; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/brk.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/brk_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/brk.tab
; Output files
;	output	html_ready/brk_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : brk
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	0	0	0	0	1	2
c	|	1	0	0	15	0	8
g	|	0	15	15	0	14	2
t	|	14	0	0	0	0	3
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	15	15	15	15	15	15	90
; c.max	|	14	15	15	15	14	8	15
; c.min	|	0	0	0	0	0	2	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	0	1	0	14	|	15	 0.93	 1.26	T	T	cTTTTTTTTTTTTTT
2	0	0	15	0	|	15	 1.00	 0.91	G	G	GGGGGGGGGGGG
3	0	0	15	0	|	15	 1.00	 0.91	G	G	GGGGGGGGGGGG
4	0	15	0	0	|	15	 1.00	 0.91	C	C	CCCCCCCCCCCC
5	1	0	14	0	|	15	 0.93	 0.75	g	g	ggggggggg
6	2	8	2	3	|	15	 0.53	 0.12	c	y	
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.0 -0.0 -0.0 -0.0 -0.1 -0.0
c	| -0.1 -0.1 -0.1  1.0 -0.1  0.2
g	| -0.1  1.0  1.0 -0.1  0.9 -0.1
t	|  1.5 -0.0 -0.0 -0.0 -0.0  0.0
;-	|-----|----|----|----|----|----|
; i.sum	|  1.3  0.9  0.9  0.9  0.7  0.1  4.8
; i.max	|  1.5  1.0  1.0  1.0  0.9  0.2  1.5
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	15
>brk_chr3R_2507229_250724
tggcgc
>brk_chr3R_2580553_258056
tggcgc
>brk_chr3R_20574945_20574
tggcgc
>brk_chr2L_11454379_11454
tggcgc
>brk_chr2L_11454460_11454
tggcgc
>brk_chrX_4231706_4231722
tggcgc
>brk_chr3R_2507343_250737
tggcgt
>brk_chr3R_20574932_20574
tggcgt
>brk_chr3R_2580147_258016
tggcgt
>brk_chr3R_2580196_258020
tggcga
>brk_chr3R_20575223_20575
tggcga
>brk_chr3R_2580282_258029
tggcgg
>brk_chr3R_2581266_258127
tggcgg
>brk_chr3R_2580051_258006
tggcac
>brk_chr3R_2507579_250759
cggcgc
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.170|c:0.330|g:0.330|t:0.170
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/brk_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	15
;	meme.llr                     	88
;	meme.E-value                 	1.5e-10
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.17
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.83974
;	information.per.column       	0.806623
;	max.possible.info.per.col    	1.77196
;	consensus.strict             	TGGCgc
;	consensus.strict.rc          	gcGCCA
;	consensus.IUPAC              	TGGCgy
;	consensus.IUPAC.rc           	rcGCCA
;	consensus.regexp             	TGGCg[ct]
;	consensus.regexp.rc          	[ag]cGCCA
;	residues.content.crude.freq  	a:0.0333|c:0.2667|g:0.5111|t:0.1889
;	G+C.content.crude.freq       	0.777778
;	residues.content.corrected.freq	a:0.0419|c:0.2706|g:0.4998|t:0.1877
;	G+C.content.corrected.freq   	0.770417
;	min(P(S|M))                  	1.83647e-11
;	max(P(S|M))                  	0.363218
;	proba_range                  	0.363218
;	Wmin                         	-14.8
;	Wmax                         	6.6
;	Wrange                       	21.4
; Job started 2007_12_10.132041
; Job done    2007_12_10.132041