; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/br-Z2.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/br-Z2_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/br-Z2.tab
; Output files
;	output	html_ready/br-Z2_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : br-Z2
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8	9	10
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	3	2	4	2	1	0	4	3	0
c	|	5	2	0	0	0	4	5	1	2	1
g	|	0	0	0	1	3	0	0	0	0	4
t	|	0	0	3	0	0	0	0	0	0	0
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	5	5	5	5	5	5	5	5	5	5	50
; c.max	|	5	3	3	4	3	4	5	4	3	4	5
; c.min	|	0	0	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	0	5	0	0	|	5	 1.00	 1.17	C	C	CCCCCCCCCCCCCCC
2	3	2	0	0	|	5	 0.60	 0.41	c	m	acc
3	2	0	0	3	|	5	 0.60	 0.24	t	w	t
4	4	0	1	0	|	5	 0.80	 0.44	a	r	aaag
5	2	0	3	0	|	5	 0.60	 0.52	G	R	aGGG
6	1	4	0	0	|	5	 0.80	 0.75	C	C	aCCCCCC
7	0	5	0	0	|	5	 1.00	 1.17	C	C	CCCCCCCCCCCCCCC
8	4	1	0	0	|	5	 0.80	 0.44	a	m	aaac
9	3	2	0	0	|	5	 0.60	 0.41	c	m	acc
10	0	1	4	0	|	5	 0.80	 0.82	G	S	cGGGGGGG
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8    9   10
;-	|-----|----|----|----|----|----|----|----|----|----|
a	| -0.1  0.3  0.1  0.6  0.1 -0.1 -0.1  0.6  0.3 -0.1
c	|  1.4  0.3 -0.0 -0.0 -0.0  1.0  1.4  0.0  0.3  0.0
g	| -0.0 -0.0 -0.0  0.0  0.6 -0.0 -0.0 -0.0 -0.0  1.0
t	| -0.1 -0.1  0.3 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|----|----|----|
; i.sum	|  1.2  0.4  0.2  0.4  0.5  0.8  1.2  0.4  0.4  0.8  6.4
; i.max	|  1.4  0.3  0.3  0.6  0.6  1.0  1.4  0.6  0.3  1.0  1.4
; i.min	| -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	5
>br-Z2_chr3L_9354293_9354
catagccaag
>br-Z2_chrX_3105784_31058
caaaaccacg
>br-Z2_chrX_3105444_31054
ccagaccacg
>br-Z2_chr2L_19116908_191
cctagcccac
>br-Z2_chrX_3105633_31056
catagacaag
;
; Matrix parameters
;	Columns                      	10
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.334|c:0.166|g:0.166|t:0.334
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/br-Z2_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	5
;	meme.llr                     	51
;	meme.E-value                 	3700
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.166
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.38314
;	information.per.column       	0.638314
;	max.possible.info.per.col    	1.79577
;	consensus.strict             	CctaGCCacG
;	consensus.strict.rc          	CgtGGCtagG
;	consensus.IUPAC              	CmwrRCCmmS
;	consensus.IUPAC.rc           	SkkGGYywkG
;	consensus.regexp             	C[ac][at][ag][AG]CC[ac][ac][CG]
;	consensus.regexp.rc          	[CG][gt][gt]GG[CT][ct][at][gt]G
;	residues.content.crude.freq  	a:0.3800|c:0.4000|g:0.1600|t:0.0600
;	G+C.content.crude.freq       	0.56
;	residues.content.corrected.freq	a:0.3723|c:0.3610|g:0.1610|t:0.1057
;	G+C.content.corrected.freq   	0.522
;	min(P(S|M))                  	5.28697e-16
;	max(P(S|M))                  	0.0168819
;	proba_range                  	0.0168819
;	Wmin                         	-18
;	Wmax                         	11
;	Wrange                       	29
; Job started 2007_12_10.132038
; Job done    2007_12_10.132038