; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Adf1.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Adf1_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Adf1.tab
; Output files
;	output	html_ready/Adf1_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Adf1
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8	9	10	11
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	0	2	2	1	0	0	0	0	1	3
c	|	0	7	2	0	5	6	0	6	0	0	4
g	|	6	0	0	5	0	0	7	0	0	6	0
t	|	1	0	3	0	1	1	0	1	7	0	0
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	7	7	7	7	7	7	7	7	7	7	7	77
; c.max	|	6	7	3	5	5	6	7	6	7	6	4	7
; c.min	|	0	0	0	0	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	0	0	6	1	|	7	 0.86	 0.52	g	g	ggggg
2	0	7	0	0	|	7	 1.00	 0.73	c	c	ccccccccc
3	2	2	0	3	|	7	 0.43	 0.37	t	w	ct
4	2	0	5	0	|	7	 0.71	 0.46	g	r	aggg
5	1	5	0	1	|	7	 0.71	 0.33	c	c	cct
6	0	6	0	1	|	7	 0.86	 0.52	c	c	ccccc
7	0	0	7	0	|	7	 1.00	 0.73	g	g	ggggggggg
8	0	6	0	1	|	7	 0.86	 0.52	c	c	ccccc
9	0	0	0	7	|	7	 1.00	 1.34	T	T	TTTTTTTTTTTTTTTTT
10	1	0	6	0	|	7	 0.86	 0.52	g	g	ggggg
11	3	4	0	0	|	7	 0.57	 0.48	a	m	acc
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8    9   10   11
;-	|-----|----|----|----|----|----|----|----|----|----|----|
a	| -0.0 -0.0  0.1  0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0  0.4
c	| -0.1  0.9 -0.0 -0.1  0.4  0.7 -0.1  0.7 -0.1 -0.1  0.2
g	|  0.7 -0.1 -0.1  0.4 -0.1 -0.1  0.9 -0.1 -0.1  0.7 -0.1
t	| -0.0 -0.0  0.4 -0.0 -0.0 -0.0 -0.0 -0.0  1.6 -0.0 -0.0
;-	|-----|----|----|----|----|----|----|----|----|----|----|
; i.sum	|  0.5  0.7  0.4  0.5  0.3  0.5  0.7  0.5  1.3  0.5  0.5  6.5
; i.max	|  0.7  0.9  0.4  0.4  0.4  0.7  0.9  0.7  1.6  0.7  0.4  1.6
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	7
>Adf1_chr2L_19116304_1911
gcagccgctga
>Adf1_chr2L_2454658_24546
gctgccgctgc
>Adf1_chr3R_2825019_28250
gccaccgctga
>Adf1_chr2L_14615473_1461
gctgctgctgc
>Adf1_chr3R_2825152_28251
gcagtcgctgc
>Adf1_chr3R_2825118_28251
gccgacgctga
>Adf1_chr2L_14616172_1461
tctaccgttac
;
; Matrix parameters
;	Columns                      	11
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.157|c:0.343|g:0.343|t:0.157
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Adf1_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	7
;	meme.llr                     	67
;	meme.E-value                 	0.031
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.157
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.54343
;	information.per.column       	0.594857
;	max.possible.info.per.col    	1.85151
;	consensus.strict             	gctgccgcTga
;	consensus.strict.rc          	tcAgcggcagc
;	consensus.IUPAC              	gcwrccgcTgm
;	consensus.IUPAC.rc           	kcAgcggywgc
;	consensus.regexp             	gc[at][ag]ccgcTg[ac]
;	consensus.regexp.rc          	[gt]cAgcgg[ct][at]gc
;	residues.content.crude.freq  	a:0.1169|c:0.3896|g:0.3117|t:0.1818
;	G+C.content.crude.freq       	0.701299
;	residues.content.corrected.freq	a:0.1219|c:0.3838|g:0.3156|t:0.1787
;	G+C.content.corrected.freq   	0.699386
;	min(P(S|M))                  	7.93771e-19
;	max(P(S|M))                  	0.0284644
;	proba_range                  	0.0284644
;	Wmin                         	-23.1
;	Wmax                         	10.2
;	Wrange                       	33.3
; Job started 2007_12_10.132029
; Job done    2007_12_10.132029