; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Antp.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Antp_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Antp.tab
; Output files
;	output	html_ready/Antp_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Antp
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	0	0	0	0	1	1
c	|	0	0	0	2	0	1
g	|	0	2	2	0	1	0
t	|	2	0	0	0	0	0
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	2	2	2	2	2	2	12
; c.max	|	2	2	2	2	1	1	2
; 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	0	0	2	|	2	 1.00	 0.32	t	t	ttt
2	0	0	2	0	|	2	 1.00	 1.10	G	G	GGGGGGGGGG
3	0	0	2	0	|	2	 1.00	 1.10	G	G	GGGGGGGGGG
4	0	2	0	0	|	2	 1.00	 1.10	C	C	CCCCCCCCCC
5	1	0	1	0	|	2	 0.50	 0.39	G	R	G
6	1	1	0	0	|	2	 0.50	 0.39	C	M	C
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.2 -0.2 -0.2 -0.2  0.1  0.1
c	| -0.0 -0.0 -0.0  1.4 -0.0  0.5
g	| -0.0  1.4  1.4 -0.0  0.5 -0.0
t	|  0.5 -0.2 -0.2 -0.2 -0.2 -0.2
;-	|-----|----|----|----|----|----|
; i.sum	|  0.3  1.1  1.1  1.1  0.4  0.4  4.4
; i.max	|  0.5  1.4  1.4  1.4  0.5  0.5  1.4
; i.min	| -0.2 -0.2 -0.2 -0.2 -0.2 -0.2 -0.2
; Sites	2
>Antp_chr2R_1216998_12170
tggcgc
>Antp_chr2R_1217540_12175
tggcaa
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.411|c:0.089|g:0.089|t:0.411
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Antp_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	2
;	meme.llr                     	20
;	meme.E-value                 	790
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.089
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.40111
;	information.per.column       	0.733518
;	max.possible.info.per.col    	2.41912
;	consensus.strict             	tGGCGC
;	consensus.strict.rc          	GCGCCa
;	consensus.IUPAC              	tGGCRM
;	consensus.IUPAC.rc           	KYGCCa
;	consensus.regexp             	tGGC[AG][AC]
;	consensus.regexp.rc          	[GT][CT]GCCa
;	residues.content.crude.freq  	a:0.1667|c:0.2500|g:0.4167|t:0.1667
;	G+C.content.crude.freq       	0.666667
;	residues.content.corrected.freq	a:0.2481|c:0.1963|g:0.3074|t:0.2481
;	G+C.content.corrected.freq   	0.503778
;	min(P(S|M))                  	6.8173e-10
;	max(P(S|M))                  	0.0600259
;	proba_range                  	0.0600259
;	Wmin                         	-6.6
;	Wmax                         	9.9
;	Wrange                       	16.5
; Job started 2007_12_10.132031
; Job done    2007_12_10.132031