; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Stat92E.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Stat92E_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Stat92E.tab
; Output files
;	output	html_ready/Stat92E_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Stat92E
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8	9
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	0	0	0	0	0	0	3	3
c	|	0	0	3	0	2	0	0	0	0
g	|	0	0	0	3	1	3	3	0	0
t	|	3	3	0	0	0	0	0	0	0
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	3	3	3	3	3	3	3	3	3	27
; c.max	|	3	3	3	3	2	3	3	3	3	3
; c.min	|	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	0	3	|	3	 1.00	 0.76	T	T	TTTTTTTTTTTT
2	0	0	0	3	|	3	 1.00	 0.76	T	T	TTTTTTTTTTTT
3	0	3	0	0	|	3	 1.00	 0.64	C	C	CCCCCCCCCC
4	0	0	3	0	|	3	 1.00	 0.64	G	G	GGGGGGGGGG
5	0	2	1	0	|	3	 0.67	 0.31	c	s	ccg
6	0	0	3	0	|	3	 1.00	 0.64	G	G	GGGGGGGGGG
7	0	0	3	0	|	3	 1.00	 0.64	G	G	GGGGGGGGGG
8	3	0	0	0	|	3	 1.00	 0.76	A	A	AAAAAAAAAAAA
9	3	0	0	0	|	3	 1.00	 0.76	A	A	AAAAAAAAAAAA
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8    9
;-	|-----|----|----|----|----|----|----|----|----|
a	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  1.0  1.0
c	| -0.1 -0.1  0.9 -0.1  0.4 -0.1 -0.1 -0.1 -0.1
g	| -0.1 -0.1 -0.1  0.9  0.0  0.9  0.9 -0.1 -0.1
t	|  1.0  1.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|----|----|
; i.sum	|  0.8  0.8  0.6  0.6  0.3  0.6  0.6  0.8  0.8  5.9
; i.max	|  1.0  1.0  0.9  0.9  0.4  0.9  0.9  1.0  1.0  1.0
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	3
>Stat92E_chrX_2196518_219
ttcgcggaa
>Stat92E_chr2R_5487511_54
ttcgcggaa
>Stat92E_chr2R_5487632_54
ttcggggaa
;
; Matrix parameters
;	Columns                      	9
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.226|c:0.274|g:0.274|t:0.226
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Stat92E_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	3
;	meme.llr                     	35
;	meme.E-value                 	0.0002
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.226
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.91368
;	information.per.column       	0.657075
;	max.possible.info.per.col    	1.48722
;	consensus.strict             	TTCGcGGAA
;	consensus.strict.rc          	TTCCgCGAA
;	consensus.IUPAC              	TTCGsGGAA
;	consensus.IUPAC.rc           	TTCCsCGAA
;	consensus.regexp             	TTCG[cg]GGAA
;	consensus.regexp.rc          	TTCC[cg]CGAA
;	residues.content.crude.freq  	a:0.2222|c:0.1852|g:0.3704|t:0.2222
;	G+C.content.crude.freq       	0.555556
;	residues.content.corrected.freq	a:0.2232|c:0.2074|g:0.3463|t:0.2232
;	G+C.content.corrected.freq   	0.553667
;	min(P(S|M))                  	5.86727e-12
;	max(P(S|M))                  	0.10795
;	proba_range                  	0.10795
;	Wmin                         	-12.6
;	Wmax                         	10.4
;	Wrange                       	23
; Job started 2007_12_10.132128
; Job done    2007_12_10.132128