; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Deaf1.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Deaf1_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Deaf1.tab
; Output files
;	output	html_ready/Deaf1_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Deaf1
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	2	5	0	0	10	7
c	|	4	5	10	0	0	0
g	|	3	0	0	10	0	3
t	|	1	0	0	0	0	0
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	10	10	10	10	10	10	60
; c.max	|	4	5	10	10	10	7	10
; c.min	|	1	0	0	0	0	0	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	2	4	3	1	|	10	 0.40	 0.07	c	s	
2	5	5	0	0	|	10	 0.50	 0.51	a	m	aacc
3	0	10	0	0	|	10	 1.00	 1.01	C	C	CCCCCCCCCCCCCCCC
4	0	0	10	0	|	10	 1.00	 1.01	G	G	GGGGGGGGGGGGGGGG
5	10	0	0	0	|	10	 1.00	 1.11	A	A	AAAAAAAAAAAAAAAAAA
6	7	0	3	0	|	10	 0.70	 0.60	A	R	AAAAggg
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.0  0.3 -0.1 -0.1  1.3  0.7
c	|  0.1  0.3  1.2 -0.1 -0.1 -0.1
g	|  0.0 -0.1 -0.1  1.2 -0.1  0.0
t	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.1  0.5  1.0  1.0  1.1  0.6  4.3
; i.max	|  0.1  0.3  1.2  1.2  1.3  0.7  1.3
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	10
>Deaf1_chr2R_2013856_2013
cacgaa
>Deaf1_chr3R_2613407_2613
cacgaa
>Deaf1_chr2R_2013751_2013
cccgaa
>Deaf1_chr3R_2613192_2613
cccgaa
>Deaf1_chr2R_2013718_2013
gccgaa
>Deaf1_chr2R_2013635_2013
aacgaa
>Deaf1_chr2R_2013613_2013
gacgag
>Deaf1_chr2R_2013811_2013
gacgag
>Deaf1_chr2R_2013899_2013
tccgaa
>Deaf1_chr2R_2013779_2013
accgag
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.235|c:0.265|g:0.265|t:0.235
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Deaf1_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	10
;	meme.llr                     	57
;	meme.E-value                 	0.073
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.235
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.32281
;	information.per.column       	0.720468
;	max.possible.info.per.col    	1.44817
;	consensus.strict             	caCGAA
;	consensus.strict.rc          	TTCGtg
;	consensus.IUPAC              	smCGAR
;	consensus.IUPAC.rc           	YTCGks
;	consensus.regexp             	[cg][ac]CGA[AG]
;	consensus.regexp.rc          	[CT]TCG[gt][cg]
;	residues.content.crude.freq  	a:0.4000|c:0.3167|g:0.2667|t:0.0167
;	G+C.content.crude.freq       	0.583333
;	residues.content.corrected.freq	a:0.3850|c:0.3120|g:0.2665|t:0.0365
;	G+C.content.corrected.freq   	0.578485
;	min(P(S|M))                  	4.99632e-10
;	max(P(S|M))                  	0.0989021
;	proba_range                  	0.0989021
;	Wmin                         	-12.7
;	Wmax                         	6.2
;	Wrange                       	18.9
; Job started 2007_12_10.132045
; Job done    2007_12_10.132045