; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/srp.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/srp_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/srp.tab
; Output files
;	output	html_ready/srp_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : srp
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	0	0	4	0	0	1
c	|	3	0	0	1	4	0
g	|	0	0	0	0	0	3
t	|	1	4	0	3	0	0
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	4	4	4	4	4	4	24
; c.max	|	3	4	4	3	4	3	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	0	3	0	1	|	4	 0.75	 0.48	C	C	CCCCt
2	0	0	0	4	|	4	 1.00	 0.76	T	T	TTTTTTTTTTTT
3	4	0	0	0	|	4	 1.00	 0.76	A	A	AAAAAAAAAAAA
4	0	1	0	3	|	4	 0.75	 0.44	t	y	ctttt
5	0	4	0	0	|	4	 1.00	 0.84	C	C	CCCCCCCCCCCCC
6	1	0	3	0	|	4	 0.75	 0.48	G	G	aGGGG
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.1 -0.1  1.0 -0.1 -0.1 -0.0
c	|  0.7 -0.1 -0.1  0.0  1.1 -0.1
g	| -0.1 -0.1 -0.1 -0.1 -0.1  0.7
t	| -0.0  1.0 -0.1  0.6 -0.1 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.5  0.8  0.8  0.4  0.8  0.5  3.8
; i.max	|  0.7  1.0  1.0  0.6  1.1  0.7  1.1
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	4
>srp_chr3L_14063390_14063
ctatcg
>srp_chrX_9898915_9898926
ctatcg
>srp_chr2L_14616180_14616
ctaccg
>srp_chr3L_14063443_14063
ttatca
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.264|c:0.236|g:0.236|t:0.264
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/srp_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	4
;	meme.llr                     	26
;	meme.E-value                 	19
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.236
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	3.76654
;	information.per.column       	0.627757
;	max.possible.info.per.col    	1.44392
;	consensus.strict             	CTAtCG
;	consensus.strict.rc          	CGaTAG
;	consensus.IUPAC              	CTAyCG
;	consensus.IUPAC.rc           	CGrTAG
;	consensus.regexp             	CTA[ct]CG
;	consensus.regexp.rc          	CG[ag]TAG
;	residues.content.crude.freq  	a:0.2083|c:0.3333|g:0.1250|t:0.3333
;	G+C.content.crude.freq       	0.458333
;	residues.content.corrected.freq	a:0.2195|c:0.3139|g:0.1472|t:0.3195
;	G+C.content.corrected.freq   	0.461067
;	min(P(S|M))                  	1.10574e-08
;	max(P(S|M))                  	0.168476
;	proba_range                  	0.168476
;	Wmin                         	-9.6
;	Wmax                         	6.7
;	Wrange                       	16.3
; Job started 2007_12_10.132127
; Job done    2007_12_10.132127