; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/br-Z3.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/br-Z3_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/br-Z3.tab
; Output files
;	output	html_ready/br-Z3_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : br-Z3
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	13	7	7	16	2	0	4	2
c	|	2	9	3	0	2	5	0	7
g	|	1	0	0	0	12	0	3	1
t	|	0	0	6	0	0	11	9	6
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	16	16	16	16	16	16	16	16	128
; c.max	|	13	9	7	16	12	11	9	7	16
; c.min	|	0	0	0	0	0	0	0	1	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	13	2	1	0	|	16	 0.81	 0.50	a	a	aaaag
2	7	9	0	0	|	16	 0.56	 0.70	C	M	aaCCC
3	7	3	0	6	|	16	 0.44	 0.13	c	h	
4	16	0	0	0	|	16	 1.00	 0.86	A	A	AAAAAAAAAA
5	2	2	12	0	|	16	 0.75	 0.92	G	G	acGGGGGG
6	0	5	0	11	|	16	 0.69	 0.56	c	y	cttt
7	4	0	3	9	|	16	 0.56	 0.18	t	k	t
8	2	7	1	6	|	16	 0.44	 0.28	C	Y	g
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	|  0.6  0.1  0.1  1.0 -0.1 -0.1 -0.1 -0.1
c	| -0.0  0.7  0.0 -0.0 -0.0  0.2 -0.0  0.4
g	| -0.1 -0.0 -0.0 -0.0  1.1 -0.0  0.0 -0.1
t	| -0.1 -0.1  0.0 -0.1 -0.1  0.4  0.2  0.0
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.5  0.7  0.1  0.9  0.9  0.6  0.2  0.3  4.1
; i.max	|  0.6  0.7  0.1  1.0  1.1  0.4  0.2  0.4  1.1
; i.min	| -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	16
>br-Z3_chrX_3105544_31055
accagctc
>br-Z3_chrX_3105939_31059
acaagttc
>br-Z3_chrX_3105849_31058
accagctt
>br-Z3_chrX_3105730_31057
actagtac
>br-Z3_chrX_3106077_31060
acaagttt
>br-Z3_chrX_3105444_31054
aaaagctc
>br-Z3_chr2L_19115597_191
aatagttt
>br-Z3_chrX_3105708_31057
aatagttt
>br-Z3_chrX_3106219_31062
cccactgc
>br-Z3_chrX_3105633_31056
cctagttg
>br-Z3_chr2L_19115461_191
gatagtgc
>br-Z3_chr2L_19115566_191
aatagtta
>br-Z3_chrX_3105784_31058
aaaaccac
>br-Z3_chr3L_9354222_9354
acaaatgt
>br-Z3_chrX_3106130_31061
aaaagtaa
>br-Z3_chr3L_9354463_9354
acaaacat
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.352|c:0.148|g:0.148|t:0.352
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/br-Z3_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	16
;	meme.llr                     	79
;	meme.E-value                 	15
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.148
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.12459
;	information.per.column       	0.515574
;	max.possible.info.per.col    	1.91054
;	consensus.strict             	aCcAGctC
;	consensus.strict.rc          	GagCTgGt
;	consensus.IUPAC              	aMhAGykY
;	consensus.IUPAC.rc           	RmrCTdKt
;	consensus.regexp             	a[AC][act]AG[ct][gt][CT]
;	consensus.regexp.rc          	[AG][ac][ag]CT[agt][GT]t
;	residues.content.crude.freq  	a:0.3984|c:0.2188|g:0.1328|t:0.2500
;	G+C.content.crude.freq       	0.351562
;	residues.content.corrected.freq	a:0.3957|c:0.2146|g:0.1337|t:0.2560
;	G+C.content.corrected.freq   	0.348294
;	min(P(S|M))                  	1.44792e-15
;	max(P(S|M))                  	0.0194054
;	proba_range                  	0.0194054
;	Wmin                         	-20.5
;	Wmax                         	7.1
;	Wrange                       	27.6
; Job started 2007_12_10.132039
; Job done    2007_12_10.132039