; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/pho.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/pho_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/pho.tab
; Output files
;	output	html_ready/pho_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : pho
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	11	0	0	0	0	0
c	|	0	0	0	0	12	5
g	|	1	0	12	12	0	1
t	|	0	12	0	0	0	6
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	12	12	12	12	12	12	72
; c.max	|	11	12	12	12	12	6	12
; 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	11	0	1	0	|	12	 0.92	 1.02	A	A	AAAAAAAAAAAAAg
2	0	0	0	12	|	12	 1.00	 1.26	T	T	TTTTTTTTTTTTTTTTTTT
3	0	0	12	0	|	12	 1.00	 0.97	G	G	GGGGGGGGGGGGGG
4	0	0	12	0	|	12	 1.00	 0.97	G	G	GGGGGGGGGGGGGG
5	0	12	0	0	|	12	 1.00	 0.97	C	C	CCCCCCCCCCCCCC
6	0	5	1	6	|	12	 0.50	 0.38	t	y	ct
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	|  1.2 -0.0 -0.0 -0.0 -0.0 -0.0
c	| -0.1 -0.1 -0.1 -0.1  1.1  0.1
g	| -0.1 -0.1  1.1  1.1 -0.1 -0.1
t	| -0.0  1.4 -0.0 -0.0 -0.0  0.4
;-	|-----|----|----|----|----|----|
; i.sum	|  1.0  1.3  1.0  1.0  1.0  0.4  5.6
; i.max	|  1.2  1.4  1.1  1.1  1.1  0.4  1.4
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	12
>pho_chr3R_12590084_12590
atggct
>pho_chr3R_12590028_12590
atggct
>pho_chr3R_12590026_12590
atggct
>pho_chr3R_12589921_12589
atggct
>pho_chr3R_12589924_12589
atggct
>pho_chr3R_12725663_12725
atggct
>pho_chr3R_12589768_12589
atggcc
>pho_chr3R_12589777_12589
atggcc
>pho_chr3R_12725704_12725
atggcc
>pho_chr3R_12589801_12589
atggcc
>pho_chr3R_12589820_12589
atggcg
>pho_chr3R_12590048_12590
gtggcc
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.208|c:0.292|g:0.292|t:0.208
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/pho_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	12
;	meme.llr                     	84
;	meme.E-value                 	1.5e-09
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.208
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.57733
;	information.per.column       	0.929554
;	max.possible.info.per.col    	1.57022
;	consensus.strict             	ATGGCt
;	consensus.strict.rc          	aGCCAT
;	consensus.IUPAC              	ATGGCy
;	consensus.IUPAC.rc           	rGCCAT
;	consensus.regexp             	ATGGC[ct]
;	consensus.regexp.rc          	[ag]GCCAT
;	residues.content.crude.freq  	a:0.1528|c:0.2361|g:0.3611|t:0.2500
;	G+C.content.crude.freq       	0.597222
;	residues.content.corrected.freq	a:0.1570|c:0.2404|g:0.3558|t:0.2468
;	G+C.content.corrected.freq   	0.596205
;	min(P(S|M))                  	1.67772e-11
;	max(P(S|M))                  	0.326838
;	proba_range                  	0.326838
;	Wmin                         	-15.6
;	Wmax                         	7.4
;	Wrange                       	23
; Job started 2007_12_10.132121
; Job done    2007_12_10.132121