; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Med.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Med_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Med.tab
; Output files
;	output	html_ready/Med_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Med
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	0	0	0	0	0	0
c	|	6	0	0	10	0	0
g	|	1	10	2	0	0	7
t	|	3	0	8	0	10	3
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	10	10	10	10	10	10	60
; c.max	|	6	10	8	10	10	7	10
; 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	0	6	1	3	|	10	 0.60	 0.33	c	y	cgt
2	0	0	10	0	|	10	 1.00	 0.95	G	G	GGGGGGGGGGGGGG
3	0	0	2	8	|	10	 0.80	 0.76	T	T	gTTTTTTTT
4	0	10	0	0	|	10	 1.00	 0.95	C	C	CCCCCCCCCCCCCC
5	0	0	0	10	|	10	 1.00	 1.20	T	T	TTTTTTTTTTTTTTTTTT
6	0	0	7	3	|	10	 0.70	 0.54	g	k	ggggt
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.0 -0.0 -0.0 -0.0 -0.0 -0.0
c	|  0.4 -0.1 -0.1  1.1 -0.1 -0.1
g	| -0.1  1.1 -0.1 -0.1 -0.1  0.6
t	|  0.1 -0.0  0.9 -0.0  1.4  0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.3  0.9  0.8  0.9  1.2  0.5  4.7
; i.max	|  0.4  1.1  0.9  1.1  1.4  0.6  1.4
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	10
>Med_chr2L_13905196_13905
cgtctg
>Med_chr2L_13905216_13905
cgtctg
>Med_chr3R_21070780_21070
tgtctg
>Med_chr2R_5497430_549745
tgtctg
>Med_chr2R_5497227_549723
cgtctt
>Med_chr3R_17209435_17209
cgtctt
>Med_chr2L_11454544_11454
cgtctt
>Med_chr2R_5497257_549726
cggctg
>Med_chr3R_17209509_17209
ggtctg
>Med_chr3R_17209380_17209
tggctg
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.213|c:0.287|g:0.287|t:0.213
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Med_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	10
;	meme.llr                     	62
;	meme.E-value                 	0.85
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.213
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.72624
;	information.per.column       	0.787706
;	max.possible.info.per.col    	1.54646
;	consensus.strict             	cGTCTg
;	consensus.strict.rc          	cAGACg
;	consensus.IUPAC              	yGTCTk
;	consensus.IUPAC.rc           	mAGACr
;	consensus.regexp             	[ct]GTCT[gt]
;	consensus.regexp.rc          	[ac]AGAC[ag]
;	residues.content.crude.freq  	a:0.0000|c:0.2667|g:0.3333|t:0.4000
;	G+C.content.crude.freq       	0.6
;	residues.content.corrected.freq	a:0.0194|c:0.2685|g:0.3291|t:0.3830
;	G+C.content.corrected.freq   	0.597636
;	min(P(S|M))                  	5.27135e-11
;	max(P(S|M))                  	0.229545
;	proba_range                  	0.229545
;	Wmin                         	-14.4
;	Wmax                         	6.8
;	Wrange                       	21.2
; Job started 2007_12_10.132115
; Job done    2007_12_10.132115