; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/SuH.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/SuH_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/SuH.tab
; Output files
;	output	html_ready/SuH_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : SuH
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	0	0	0	1	0	3
c	|	0	0	3	1	3	0
g	|	0	0	0	0	0	0
t	|	3	3	0	1	0	0
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	3	3	3	3	3	3	18
; c.max	|	3	3	3	1	3	3	3
; 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	3	|	3	 1.00	 0.62	T	T	TTTTTTTTT
2	0	0	0	3	|	3	 1.00	 0.62	T	T	TTTTTTTTT
3	0	3	0	0	|	3	 1.00	 0.79	C	C	CCCCCCCCCCCC
4	1	1	0	1	|	3	 0.33	 0.11	c	h	
5	0	3	0	0	|	3	 1.00	 0.79	C	C	CCCCCCCCCCCC
6	3	0	0	0	|	3	 1.00	 0.62	A	A	AAAAAAAAA
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.1 -0.1 -0.1  0.0 -0.1  0.9
c	| -0.1 -0.1  1.1  0.1  1.1 -0.1
g	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
t	|  0.9  0.9 -0.1  0.0 -0.1 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.6  0.6  0.8  0.1  0.8  0.6  3.5
; i.max	|  0.9  0.9  1.1  0.1  1.1  0.9  1.1
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	3
>Su(H)_chr3R_22997565_229
ttccca
>Su(H)_chr2R_8404876_8404
ttctca
>Su(H)_chr3R_22997585_229
ttcaca
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.286|c:0.214|g:0.214|t:0.286
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/SuH_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	3
;	meme.llr                     	21
;	meme.E-value                 	2.6
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.214
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	3.54639
;	information.per.column       	0.591066
;	max.possible.info.per.col    	1.54178
;	consensus.strict             	TTCcCA
;	consensus.strict.rc          	TGgGAA
;	consensus.IUPAC              	TTChCA
;	consensus.IUPAC.rc           	TGdGAA
;	consensus.regexp             	TTC[act]CA
;	consensus.regexp.rc          	TG[agt]GAA
;	residues.content.crude.freq  	a:0.2222|c:0.3889|g:0.0000|t:0.3889
;	G+C.content.crude.freq       	0.388889
;	residues.content.corrected.freq	a:0.2382|c:0.3452|g:0.0535|t:0.3632
;	G+C.content.corrected.freq   	0.398667
;	min(P(S|M))                  	2.34489e-08
;	max(P(S|M))                  	0.115074
;	proba_range                  	0.115074
;	Wmin                         	-8.4
;	Wmax                         	6.3
;	Wrange                       	14.7
; Job started 2007_12_10.132129
; Job done    2007_12_10.132129