; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/twi.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/twi_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/twi.tab
; Output files
;	output	html_ready/twi_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : twi
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	1	15	2	12	0	0
c	|	14	0	7	3	3	0
g	|	0	0	1	0	2	14
t	|	0	0	5	0	10	1
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	15	15	15	15	15	15	90
; c.max	|	14	15	7	12	10	14	15
; c.min	|	0	0	1	0	0	0	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	1	14	0	0	|	15	 0.93	 0.98	C	C	aCCCCCCCCCCCCCC
2	15	0	0	0	|	15	 1.00	 1.12	A	A	AAAAAAAAAAAAAAAAAA
3	2	7	1	5	|	15	 0.47	 0.19	c	y	t
4	12	3	0	0	|	15	 0.80	 0.71	A	A	AAAAAAAcc
5	0	3	2	10	|	15	 0.67	 0.43	t	t	gttt
6	0	0	14	1	|	15	 0.93	 0.98	G	G	GGGGGGGGGGGGGGt
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.1  1.2 -0.1  0.8 -0.0 -0.0
c	|  1.2 -0.0  0.3 -0.0 -0.0 -0.0
g	| -0.0 -0.0 -0.1 -0.0 -0.1  1.2
t	| -0.0 -0.0  0.1 -0.0  0.6 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  1.0  1.1  0.2  0.7  0.4  1.0  4.4
; i.max	|  1.2  1.2  0.3  0.8  0.6  1.2  1.2
; i.min	| -0.1 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1
; Sites	15
>twi_chr3R_17205813_17205
cacatg
>twi_chr3R_12527019_12527
cacatg
>twi_chr3L_1445555_144556
cacatg
>twi_chr3R_17205973_17205
catatg
>twi_chr3R_17203833_17203
catatg
>twi_chr3R_8895842_889584
catatg
>twi_chr3L_1445544_144555
catatg
>twi_chr2L_15474287_15474
cacacg
>twi_chr3R_12526730_12526
cacacg
>twi_chr3R_8895908_889591
cacctg
>twi_chr2L_15474247_15474
caaatg
>twi_chr3R_12526900_12526
cacatt
>twi_chr3R_12526987_12527
catcgg
>twi_chr3R_12599153_12599
cagccg
>twi_chr3R_12599116_12599
aaaagg
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.258|c:0.242|g:0.242|t:0.258
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/twi_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	15
;	meme.llr                     	79
;	meme.E-value                 	1e-06
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.242
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.40366
;	information.per.column       	0.733944
;	max.possible.info.per.col    	1.41882
;	consensus.strict             	CAcAtG
;	consensus.strict.rc          	CaTgTG
;	consensus.IUPAC              	CAyAtG
;	consensus.IUPAC.rc           	CaTrTG
;	consensus.regexp             	CA[ct]AtG
;	consensus.regexp.rc          	CaT[ag]TG
;	residues.content.crude.freq  	a:0.3333|c:0.3000|g:0.1889|t:0.1778
;	G+C.content.crude.freq       	0.488889
;	residues.content.corrected.freq	a:0.3286|c:0.2964|g:0.1922|t:0.1828
;	G+C.content.corrected.freq   	0.488583
;	min(P(S|M))                  	6.55063e-11
;	max(P(S|M))                  	0.167981
;	proba_range                  	0.167981
;	Wmin                         	-15.1
;	Wmax                         	6.6
;	Wrange                       	21.7
; Job started 2007_12_10.132137
; Job done    2007_12_10.132137