; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/prd.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/prd_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/prd.tab
; Output files
;	output	html_ready/prd_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : prd
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	5	0	0	3	0	9	7
c	|	6	0	8	5	2	7	0	2
g	|	0	4	1	4	4	2	0	0
t	|	3	0	0	0	0	0	0	0
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	9	9	9	9	9	9	9	9	72
; c.max	|	6	5	8	5	4	7	9	7	9
; c.min	|	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	6	0	3	|	9	 0.67	 0.57	c	y	cccctt
2	5	0	4	0	|	9	 0.56	 0.50	a	r	aagg
3	0	8	1	0	|	9	 0.89	 0.84	C	C	CCCCCCCCCCgg
4	0	5	4	0	|	9	 0.56	 0.56	c	s	ccgg
5	3	2	4	0	|	9	 0.44	 0.25	g	r	c
6	0	7	2	0	|	9	 0.78	 0.69	C	C	CCCCCCgg
7	9	0	0	0	|	9	 1.00	 0.98	A	A	AAAAAAAAAAAAAAAA
8	7	2	0	0	|	9	 0.78	 0.60	a	a	aaaaaac
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	| -0.1  0.4 -0.1 -0.1  0.1 -0.1  1.1  0.7
c	|  0.6 -0.1  1.0  0.4 -0.0  0.8 -0.1 -0.0
g	| -0.1  0.3 -0.1  0.3  0.3 -0.0 -0.1 -0.1
t	|  0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.6  0.5  0.8  0.6  0.2  0.7  1.0  0.6  5.0
; i.max	|  0.6  0.4  1.0  0.4  0.3  0.8  1.1  0.7  1.1
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	9
>prd_chr2R_20564538_20564
caccgcaa
>prd_chr2R_20564499_20564
taccgcaa
>prd_chr2R_20564927_20564
cacgccaa
>prd_chr2R_5490991_549101
caccgcac
>prd_chr2R_20564465_20564
cgccggaa
>prd_chr2R_20564736_20564
tgcgacaa
>prd_chr2R_20564632_20564
cacccgaa
>prd_chr2R_20564846_20564
tgcgacac
>prd_chr2R_5490918_549095
cgggacaa
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.268|c:0.232|g:0.232|t:0.268
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/prd_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	9
;	meme.llr                     	61
;	meme.E-value                 	30
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.232
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.98018
;	information.per.column       	0.622522
;	max.possible.info.per.col    	1.46102
;	consensus.strict             	caCcgCAa
;	consensus.strict.rc          	tTGcgGtg
;	consensus.IUPAC              	yrCsrCAa
;	consensus.IUPAC.rc           	tTGysGyr
;	consensus.regexp             	[ct][ag]C[cg][ag]CAa
;	consensus.regexp.rc          	tTG[ct][cg]G[ct][ag]
;	residues.content.crude.freq  	a:0.3333|c:0.4167|g:0.2083|t:0.0417
;	G+C.content.crude.freq       	0.625
;	residues.content.corrected.freq	a:0.3268|c:0.3982|g:0.2107|t:0.0643
;	G+C.content.corrected.freq   	0.6089
;	min(P(S|M))                  	1.49448e-13
;	max(P(S|M))                  	0.0291509
;	proba_range                  	0.0291509
;	Wmin                         	-18.4
;	Wmax                         	7.8
;	Wrange                       	26.2
; Job started 2007_12_10.132123
; Job done    2007_12_10.132123