; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/His2B.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/His2B_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/His2B.tab
; Output files
;	output	html_ready/His2B_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : His2B
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	4	1	1	0	2	4
c	|	1	0	4	1	0	0
g	|	0	4	0	1	1	1
t	|	0	0	0	3	2	0
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	5	5	5	5	5	5	30
; c.max	|	4	4	4	3	2	4	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	1	0	0	|	5	 0.80	 0.49	a	a	aaaaaac
2	1	0	4	0	|	5	 0.80	 0.63	G	G	aGGGGGGGG
3	1	4	0	0	|	5	 0.80	 0.63	C	C	aCCCCCCCC
4	0	1	1	3	|	5	 0.60	 0.25	t	t	gt
5	2	0	1	2	|	5	 0.40	 0.14	a	w	t
6	4	0	1	0	|	5	 0.80	 0.49	a	a	aaaaaag
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	|  0.7 -0.1 -0.1 -0.1  0.1  0.7
c	| -0.0 -0.1  0.8 -0.0 -0.1 -0.1
g	| -0.1  0.8 -0.1 -0.0 -0.0 -0.0
t	| -0.1 -0.1 -0.1  0.4  0.1 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.5  0.6  0.6  0.2  0.1  0.5  2.6
; i.max	|  0.7  0.8  0.8  0.4  0.1  0.7  0.8
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	5
>His2B_chr3L_20631203_206
agctta
>His2B_chr3L_20631214_206
agctga
>His2B_chr3L_20631244_206
agccag
>His2B_chr3L_20631233_206
aacgaa
>His2B_chr3L_20631225_206
cgatta
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.287|c:0.212|g:0.212|t:0.287
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/His2B_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	5
;	meme.llr                     	21
;	meme.E-value                 	3.6
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.212
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	2.63616
;	information.per.column       	0.439361
;	max.possible.info.per.col    	1.55117
;	consensus.strict             	aGCtaa
;	consensus.strict.rc          	ttaGCt
;	consensus.IUPAC              	aGCtwa
;	consensus.IUPAC.rc           	twaGCt
;	consensus.regexp             	aGCt[at]a
;	consensus.regexp.rc          	t[at]aGCt
;	residues.content.crude.freq  	a:0.4000|c:0.2000|g:0.2333|t:0.1667
;	G+C.content.crude.freq       	0.433333
;	residues.content.corrected.freq	a:0.3812|c:0.2020|g:0.2298|t:0.1867
;	G+C.content.corrected.freq   	0.431778
;	min(P(S|M))                  	2.63423e-09
;	max(P(S|M))                  	0.0525342
;	proba_range                  	0.0525342
;	Wmin                         	-10.8
;	Wmax                         	5.2
;	Wrange                       	16
; Job started 2007_12_10.132107
; Job done    2007_12_10.132107