; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/abd-A.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/abd-A_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/abd-A.tab
; Output files
;	output	html_ready/abd-A_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : abd-A
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	0	0	0	1	0	0	5
c	|	0	0	1	4	1	0	6	1
g	|	0	6	5	0	0	2	0	0
t	|	6	0	0	2	4	4	0	0
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	6	6	6	6	6	6	6	6	48
; c.max	|	6	6	5	4	4	4	6	5	6
; c.min	|	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	6	|	6	 1.00	 0.64	t	t	ttttttt
2	0	0	6	0	|	6	 1.00	 1.43	G	G	GGGGGGGGGGGGGGGG
3	0	1	5	0	|	6	 0.83	 1.10	G	S	cGGGGGGGGG
4	0	4	0	2	|	6	 0.67	 0.73	C	C	CCCtt
5	1	1	0	4	|	6	 0.67	 0.20	t	y	t
6	0	0	2	4	|	6	 0.67	 0.45	g	k	gtt
7	0	6	0	0	|	6	 1.00	 1.43	C	C	CCCCCCCCCCCCCCCC
8	5	1	0	0	|	6	 0.83	 0.45	a	m	aaac
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  0.6
c	| -0.0 -0.0  0.0  0.9  0.0 -0.0  1.7  0.0
g	| -0.0  1.7  1.3 -0.0 -0.0  0.3 -0.0 -0.0
t	|  0.8 -0.1 -0.1 -0.0  0.3  0.3 -0.1 -0.1
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.6  1.4  1.1  0.7  0.2  0.4  1.4  0.5  6.4
; i.max	|  0.8  1.7  1.3  0.9  0.3  0.3  1.7  0.6  1.7
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	6
>abd-A_chr3R_2760146_2760
tggcttca
>abd-A_chr3R_2760074_2760
tggcttca
>abd-A_chr2L_2446071_2446
tggcttcc
>abd-A_chr3R_2759631_2759
tggcagca
>abd-A_chr2L_2445914_2445
tggtcgca
>abd-A_chr3R_2759484_2759
tgctttca
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.371|c:0.129|g:0.129|t:0.371
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/abd-A_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	6
;	meme.llr                     	57
;	meme.E-value                 	1100
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.129
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.44214
;	information.per.column       	0.805267
;	max.possible.info.per.col    	2.04794
;	consensus.strict             	tGGCtgCa
;	consensus.strict.rc          	tGcaGCCa
;	consensus.IUPAC              	tGSCykCm
;	consensus.IUPAC.rc           	kGmrGSCa
;	consensus.regexp             	tG[CG]C[ct][gt]C[ac]
;	consensus.regexp.rc          	[gt]G[ac][ag]G[CG]Ca
;	residues.content.crude.freq  	a:0.1250|c:0.2708|g:0.2708|t:0.3333
;	G+C.content.crude.freq       	0.541667
;	residues.content.corrected.freq	a:0.1601|c:0.2506|g:0.2506|t:0.3387
;	G+C.content.corrected.freq   	0.501143
;	min(P(S|M))                  	3.82576e-14
;	max(P(S|M))                  	0.0902188
;	proba_range                  	0.0902188
;	Wmin                         	-15.2
;	Wmax                         	10.1
;	Wrange                       	25.3
; Job started 2007_12_10.132026
; Job done    2007_12_10.132026