; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ttk.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/ttk_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ttk.tab
; Output files
;	output	html_ready/ttk_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : ttk
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7
; -----	|--------|-------|-------|-------|-------|-------|-------|
a	|	3	7	0	0	8	0	3
c	|	5	0	0	0	0	5	5
g	|	0	1	8	8	0	0	0
t	|	0	0	0	0	0	3	0
; -----	|--------|-------|-------|-------|-------|-------|-------|
; c.sum	|	8	8	8	8	8	8	8	56
; c.max	|	5	7	8	8	8	5	5	8
; c.min	|	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	3	5	0	0	|	8	 0.62	 0.48	c	m	accc
2	7	0	1	0	|	8	 0.88	 0.86	A	A	AAAAAAAAAAg
3	0	0	8	0	|	8	 1.00	 0.88	G	G	GGGGGGGGGGGGG
4	0	0	8	0	|	8	 1.00	 0.88	G	G	GGGGGGGGGGGGG
5	8	0	0	0	|	8	 1.00	 1.16	A	A	AAAAAAAAAAAAAAAAA
6	0	5	0	3	|	8	 0.62	 0.48	c	y	cctt
7	3	5	0	0	|	8	 0.62	 0.48	c	m	accc
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7
;-	|-----|----|----|----|----|----|----|
a	|  0.2  1.1 -0.1 -0.1  1.4 -0.1  0.2
c	|  0.4 -0.1 -0.1 -0.1 -0.1  0.4  0.4
g	| -0.1 -0.1  1.1  1.1 -0.1 -0.1 -0.1
t	| -0.1 -0.1 -0.1 -0.1 -0.1  0.2 -0.1
;-	|-----|----|----|----|----|----|----|
; i.sum	|  0.5  0.9  0.9  0.9  1.2  0.5  0.5  5.2
; i.max	|  0.4  1.1  1.1  1.1  1.4  0.4  0.4  1.4
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	8
>ttk_chr2R_5485831_548584
caggacc
>ttk_chr3R_2689863_268988
caggacc
>ttk_chr2R_5490854_549088
caggacc
>ttk_chr2R_5490909_549092
caggacc
>ttk_chr3R_26677882_26677
caggatc
>ttk_chr3R_2689897_268991
aaggaca
>ttk_chr3R_2685247_268526
aaggata
>ttk_chr3R_2689955_268997
agggata
;
; Matrix parameters
;	Columns                      	7
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.206|c:0.294|g:0.294|t:0.206
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/ttk_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	8
;	meme.llr                     	58
;	meme.E-value                 	0.00041
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.206
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.22842
;	information.per.column       	0.746917
;	max.possible.info.per.col    	1.57988
;	consensus.strict             	cAGGAcc
;	consensus.strict.rc          	ggTCCTg
;	consensus.IUPAC              	mAGGAym
;	consensus.IUPAC.rc           	krTCCTk
;	consensus.regexp             	[ac]AGGA[ct][ac]
;	consensus.regexp.rc          	[gt][ag]TCCT[gt]
;	residues.content.crude.freq  	a:0.3750|c:0.2679|g:0.3036|t:0.0536
;	G+C.content.crude.freq       	0.571429
;	residues.content.corrected.freq	a:0.3562|c:0.2708|g:0.3025|t:0.0705
;	G+C.content.corrected.freq   	0.57327
;	min(P(S|M))                  	3.29134e-12
;	max(P(S|M))                  	0.126185
;	proba_range                  	0.126185
;	Wmin                         	-15.4
;	Wmax                         	7.3
;	Wrange                       	22.7
; Job started 2007_12_10.132136
; Job done    2007_12_10.132136