; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/nub.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/nub_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/nub.tab
; Output files
;	output	html_ready/nub_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : nub
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	0	3	0	1	0	4	2	0
c	|	0	0	0	1	3	0	0	0
g	|	0	0	0	2	0	0	1	4
t	|	4	1	4	0	1	0	1	0
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	4	4	4	4	4	4	4	4	32
; c.max	|	4	3	4	2	3	4	2	4	4
; 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	4	|	4	 1.00	 0.78	T	T	TTTTTTTTTTTTT
2	3	0	0	1	|	4	 0.75	 0.44	a	a	aaaat
3	0	0	0	4	|	4	 1.00	 0.78	T	T	TTTTTTTTTTTTT
4	1	1	2	0	|	4	 0.50	 0.19	g	s	g
5	0	3	0	1	|	4	 0.75	 0.47	c	c	cccct
6	4	0	0	0	|	4	 1.00	 0.78	A	A	AAAAAAAAAAAAA
7	2	0	1	1	|	4	 0.50	 0.18	a	r	g
8	0	0	4	0	|	4	 1.00	 0.82	G	G	GGGGGGGGGGGGG
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	| -0.1  0.6 -0.1 -0.0 -0.1  1.0  0.3 -0.1
c	| -0.1 -0.1 -0.1  0.0  0.6 -0.1 -0.1 -0.1
g	| -0.1 -0.1 -0.1  0.3 -0.1 -0.1  0.0  1.1
t	|  1.0 -0.0  1.0 -0.1 -0.0 -0.1 -0.0 -0.1
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.8  0.4  0.8  0.2  0.5  0.8  0.2  0.8  4.4
; i.max	|  1.0  0.6  1.0  0.3  0.6  1.0  0.3  1.1  1.1
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	4
>nub_chr2R_8405041_840505
tatacaag
>nub_chr2R_8405078_840509
tatgtaag
>nub_chr2R_8405152_840516
tatccagg
>nub_chr2R_8405118_840513
tttgcatg
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.258|c:0.242|g:0.242|t:0.258
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/nub_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	4
;	meme.llr                     	31
;	meme.E-value                 	11
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.242
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.43668
;	information.per.column       	0.554585
;	max.possible.info.per.col    	1.41882
;	consensus.strict             	TaTgcAaG
;	consensus.strict.rc          	CtTgcAtA
;	consensus.IUPAC              	TaTscArG
;	consensus.IUPAC.rc           	CyTgsAtA
;	consensus.regexp             	TaT[cg]cA[ag]G
;	consensus.regexp.rc          	C[ct]Tg[cg]AtA
;	residues.content.crude.freq  	a:0.3125|c:0.1250|g:0.2188|t:0.3438
;	G+C.content.crude.freq       	0.34375
;	residues.content.corrected.freq	a:0.3016|c:0.1484|g:0.2234|t:0.3266
;	G+C.content.corrected.freq   	0.3718
;	min(P(S|M))                  	3.21046e-11
;	max(P(S|M))                  	0.0448282
;	proba_range                  	0.0448282
;	Wmin                         	-12.8
;	Wmax                         	8.1
;	Wrange                       	20.9
; Job started 2007_12_10.132117
; Job done    2007_12_10.132117