; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/tin.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/tin_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/tin.tab
; Output files
;	output	html_ready/tin_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : tin
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	10	0	0	0	2	10
c	|	1	11	0	0	1	0
g	|	0	0	0	0	8	1
t	|	0	0	11	11	0	0
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	11	11	11	11	11	11	66
; c.max	|	10	11	11	11	8	10	11
; 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	10	1	0	0	|	11	 0.91	 0.85	A	A	AAAAAAAAAAAAc
2	0	11	0	0	|	11	 1.00	 1.08	C	C	CCCCCCCCCCCCCCCCCC
3	0	0	0	11	|	11	 1.00	 1.08	T	T	TTTTTTTTTTTTTTTTTT
4	0	0	0	11	|	11	 1.00	 1.08	T	T	TTTTTTTTTTTTTTTTTT
5	2	1	8	0	|	11	 0.73	 0.50	G	G	aGGGGG
6	10	0	1	0	|	11	 0.91	 0.85	A	A	AAAAAAAAAAAAg
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	|  1.0 -0.1 -0.1 -0.1 -0.1  1.0
c	| -0.1  1.2 -0.1 -0.1 -0.1 -0.1
g	| -0.1 -0.1 -0.1 -0.1  0.7 -0.1
t	| -0.1 -0.1  1.2  1.2 -0.1 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.9  1.1  1.1  1.1  0.5  0.9  5.5
; i.max	|  1.0  1.2  1.2  1.2  0.7  1.0  1.2
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	11
>tin_chr2R_19816868_19816
acttga
>tin_chr2R_5497516_549752
acttga
>tin_chr3R_17209345_17209
acttga
>tin_chr2R_5447129_544713
acttga
>tin_chr2R_19811989_19812
acttga
>tin_chr3R_17209536_17209
acttga
>tin_chr2R_5447302_544731
acttga
>tin_chr2R_5497350_549735
acttaa
>tin_chr2R_5497333_549733
acttca
>tin_chr2R_5497461_549746
ccttga
>tin_chr2R_19812026_19812
acttag
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.250|c:0.250|g:0.250|t:0.250
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/tin_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	11
;	meme.llr                     	76
;	meme.E-value                 	5.7e-13
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.25
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.4596
;	information.per.column       	0.909933
;	max.possible.info.per.col    	1.38629
;	consensus.strict             	ACTTGA
;	consensus.strict.rc          	TCAAGT
;	consensus.IUPAC              	ACTTGA
;	consensus.IUPAC.rc           	TCAAGT
;	consensus.regexp             	ACTTGA
;	consensus.regexp.rc          	TCAAGT
;	residues.content.crude.freq  	a:0.3333|c:0.1970|g:0.1364|t:0.3333
;	G+C.content.crude.freq       	0.333333
;	residues.content.corrected.freq	a:0.3264|c:0.2014|g:0.1458|t:0.3264
;	G+C.content.corrected.freq   	0.347222
;	min(P(S|M))                  	8.17622e-11
;	max(P(S|M))                  	0.413306
;	proba_range                  	0.413306
;	Wmin                         	-15
;	Wmax                         	7.4
;	Wrange                       	22.4
; Job started 2007_12_10.132130
; Job done    2007_12_10.132130