; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/br-Z4.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/br-Z4_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/br-Z4.tab
; Output files
;	output	html_ready/br-Z4_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : br-Z4
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	4	0	0	1	0	0
c	|	0	1	3	0	3	0
g	|	0	3	0	0	1	3
t	|	0	0	1	3	0	1
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	4	4	4	4	4	4	24
; c.max	|	4	3	3	3	3	3	4
; 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	4	0	0	0	|	4	 1.00	 0.56	a	a	aaaaaa
2	0	1	3	0	|	4	 0.75	 0.85	G	S	cGGGGGG
3	0	3	0	1	|	4	 0.75	 0.73	C	C	CCCCtt
4	1	0	0	3	|	4	 0.75	 0.24	t	t	tt
5	0	3	1	0	|	4	 0.75	 0.85	C	S	CCCCCgg
6	0	0	3	1	|	4	 0.75	 0.73	G	G	GGGGtt
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	|  0.8 -0.1 -0.1 -0.1 -0.1 -0.1
c	| -0.0  0.1  1.0 -0.0  1.0 -0.0
g	| -0.0  1.0 -0.0 -0.0  0.1  1.0
t	| -0.1 -0.1 -0.1  0.4 -0.1 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.6  0.9  0.7  0.2  0.9  0.7  4.0
; i.max	|  0.8  1.0  1.0  0.4  1.0  1.0  1.0
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	4
>br-Z4_chrX_3105849_31058
agctgg
>br-Z4_chr2L_19115393_191
agctct
>br-Z4_chrX_3105915_31059
agttcg
>br-Z4_chrX_3105784_31058
accacg
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.366|c:0.134|g:0.134|t:0.366
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/br-Z4_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	4
;	meme.llr                     	27
;	meme.E-value                 	1000
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.134
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	3.95316
;	information.per.column       	0.658859
;	max.possible.info.per.col    	2.00992
;	consensus.strict             	aGCtCG
;	consensus.strict.rc          	CGaGCt
;	consensus.IUPAC              	aSCtSG
;	consensus.IUPAC.rc           	CSaGSt
;	consensus.regexp             	a[CG]Ct[CG]G
;	consensus.regexp.rc          	C[CG]aG[CG]t
;	residues.content.crude.freq  	a:0.2083|c:0.2917|g:0.2917|t:0.2083
;	G+C.content.crude.freq       	0.583333
;	residues.content.corrected.freq	a:0.2399|c:0.2601|g:0.2601|t:0.2399
;	G+C.content.corrected.freq   	0.520267
;	min(P(S|M))                  	2.76415e-09
;	max(P(S|M))                  	0.0907348
;	proba_range                  	0.0907348
;	Wmin                         	-9.6
;	Wmax                         	7.6
;	Wrange                       	17.2
; Job started 2007_12_10.132040
; Job done    2007_12_10.132040