; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Aef1.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Aef1_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Aef1.tab
; Output files
;	output	html_ready/Aef1_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Aef1
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7
; -----	|--------|-------|-------|-------|-------|-------|-------|
a	|	0	3	3	0	2	3	0
c	|	3	0	0	3	0	0	3
g	|	0	0	0	0	0	0	0
t	|	0	0	0	0	1	0	0
; -----	|--------|-------|-------|-------|-------|-------|-------|
; c.sum	|	3	3	3	3	3	3	3	21
; c.max	|	3	3	3	3	2	3	3	3
; c.min	|	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	3	0	0	|	3	 1.00	 0.77	C	C	CCCCCCCCCCCC
2	3	0	0	0	|	3	 1.00	 0.63	A	A	AAAAAAAAAA
3	3	0	0	0	|	3	 1.00	 0.63	A	A	AAAAAAAAAA
4	0	3	0	0	|	3	 1.00	 0.77	C	C	CCCCCCCCCCCC
5	2	0	0	1	|	3	 0.67	 0.30	a	w	aat
6	3	0	0	0	|	3	 1.00	 0.63	A	A	AAAAAAAAAA
7	0	3	0	0	|	3	 1.00	 0.77	C	C	CCCCCCCCCCCC
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7
;-	|-----|----|----|----|----|----|----|
a	| -0.1  0.9  0.9 -0.1  0.4  0.9 -0.1
c	|  1.0 -0.1 -0.1  1.0 -0.1 -0.1  1.0
g	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
t	| -0.1 -0.1 -0.1 -0.1  0.0 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|
; i.sum	|  0.8  0.6  0.6  0.8  0.3  0.6  0.8  4.5
; i.max	|  1.0  0.9  0.9  1.0  0.4  0.9  1.0  1.0
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	3
>Aef1_chr2L_14615019_1461
caacaac
>Aef1_chr2L_14616265_1461
caacaac
>Aef1_chrX_9898769_989878
caactac
;
; Matrix parameters
;	Columns                      	7
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.279|c:0.221|g:0.221|t:0.279
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Aef1_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	3
;	meme.llr                     	27
;	meme.E-value                 	3.5
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.221
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.51171
;	information.per.column       	0.64453
;	max.possible.info.per.col    	1.50959
;	consensus.strict             	CAACaAC
;	consensus.strict.rc          	GTtGTTG
;	consensus.IUPAC              	CAACwAC
;	consensus.IUPAC.rc           	GTwGTTG
;	consensus.regexp             	CAAC[at]AC
;	consensus.regexp.rc          	GT[at]GTTG
;	residues.content.crude.freq  	a:0.5238|c:0.4286|g:0.0000|t:0.0476
;	G+C.content.crude.freq       	0.428571
;	residues.content.corrected.freq	a:0.4626|c:0.3767|g:0.0553|t:0.1055
;	G+C.content.corrected.freq   	0.431929
;	min(P(S|M))                  	1.57154e-09
;	max(P(S|M))                  	0.163878
;	proba_range                  	0.163878
;	Wmin                         	-9.8
;	Wmax                         	8
;	Wrange                       	17.8
; Job started 2007_12_10.132030
; Job done    2007_12_10.132030