; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ftz-f1.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/ftz-f1_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ftz-f1.tab
; Output files
;	output	html_ready/ftz-f1_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : ftz-f1
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7
; -----	|--------|-------|-------|-------|-------|-------|-------|
a	|	0	0	3	0	0	0	0
c	|	1	0	0	4	4	0	0
g	|	0	4	0	0	0	0	0
t	|	3	0	1	0	0	4	4
; -----	|--------|-------|-------|-------|-------|-------|-------|
; c.sum	|	4	4	4	4	4	4	4	28
; c.max	|	3	4	3	4	4	4	4	4
; 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	1	0	3	|	4	 0.75	 0.54	T	T	cTTTTT
2	0	0	4	0	|	4	 1.00	 0.69	G	G	GGGGGGGGGG
3	3	0	0	1	|	4	 0.75	 0.58	A	W	AAAAtt
4	0	4	0	0	|	4	 1.00	 0.69	C	C	CCCCCCCCCC
5	0	4	0	0	|	4	 1.00	 0.69	C	C	CCCCCCCCCC
6	0	0	0	4	|	4	 1.00	 0.93	T	T	TTTTTTTTTTTTTT
7	0	0	0	4	|	4	 1.00	 0.93	T	T	TTTTTTTTTTTTTT
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7
;-	|-----|----|----|----|----|----|----|
a	| -0.1 -0.1  0.7 -0.1 -0.1 -0.1 -0.1
c	| -0.0 -0.1 -0.1  0.9  0.9 -0.1 -0.1
g	| -0.1  0.9 -0.1 -0.1 -0.1 -0.1 -0.1
t	|  0.7 -0.1  0.0 -0.1 -0.1  1.2  1.2
;-	|-----|----|----|----|----|----|----|
; i.sum	|  0.5  0.7  0.6  0.7  0.7  0.9  0.9  5.1
; i.max	|  0.7  0.9  0.7  0.9  0.9  1.2  1.2  1.2
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	4
>ftz-f1_chr2R_7041814_704
tgacctt
>ftz-f1_chr3R_2510067_251
tgacctt
>ftz-f1_chr2R_7042039_704
tgtcctt
>ftz-f1_chr3R_2689754_268
cgacctt
;
; Matrix parameters
;	Columns                      	7
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.204|c:0.296|g:0.296|t:0.204
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/ftz-f1_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	4
;	meme.llr                     	35
;	meme.E-value                 	0.0014
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.204
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.05701
;	information.per.column       	0.722429
;	max.possible.info.per.col    	1.58964
;	consensus.strict             	TGACCTT
;	consensus.strict.rc          	AAGGTCA
;	consensus.IUPAC              	TGWCCTT
;	consensus.IUPAC.rc           	AAGGWCA
;	consensus.regexp             	TG[AT]CCTT
;	consensus.regexp.rc          	AAGG[AT]CA
;	residues.content.crude.freq  	a:0.1071|c:0.3214|g:0.1429|t:0.4286
;	G+C.content.crude.freq       	0.464286
;	residues.content.corrected.freq	a:0.1265|c:0.3163|g:0.1735|t:0.3837
;	G+C.content.corrected.freq   	0.489829
;	min(P(S|M))                  	2.73075e-10
;	max(P(S|M))                  	0.184125
;	proba_range                  	0.184125
;	Wmin                         	-11.2
;	Wmax                         	8.4
;	Wrange                       	19.6
; Job started 2007_12_10.132059
; Job done    2007_12_10.132059