; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ap.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/ap_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ap.tab
; Output files
;	output	html_ready/ap_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : ap
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	1	4	12	0	0	7
c	|	1	1	1	0	0	2
g	|	0	4	1	0	0	4
t	|	12	5	0	14	14	1
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	14	14	14	14	14	14	84
; c.max	|	12	5	12	14	14	7	14
; c.min	|	0	1	0	0	0	1	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	1	1	0	12	|	14	 0.86	 0.47	t	t	tttt
2	4	1	4	5	|	14	 0.36	 0.08	g	g	
3	12	1	1	0	|	14	 0.86	 0.51	a	a	aaaag
4	0	0	0	14	|	14	 1.00	 0.80	t	t	ttttttttt
5	0	0	0	14	|	14	 1.00	 0.80	t	t	ttttttttt
6	7	2	4	1	|	14	 0.50	 0.23	g	v	g
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.1 -0.1  0.7 -0.1 -0.1  0.1
c	| -0.0 -0.0 -0.0 -0.0 -0.0  0.0
g	| -0.0  0.2 -0.0 -0.0 -0.0  0.2
t	|  0.7 -0.0 -0.1  0.9  0.9 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.5  0.1  0.5  0.8  0.8  0.2  2.9
; i.max	|  0.7  0.2  0.7  0.9  0.9  0.2  0.9
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	14
>ap_chr3R_22997174_229971
tgattg
>ap_chr3R_22997731_229977
tgattg
>ap_chr3R_22997776_229977
tgatta
>ap_chr3R_22997594_229976
taattg
>ap_chr3R_22997795_229978
ttatta
>ap_chr3R_22997027_229970
ttatta
>ap_chr3R_22997413_229974
taatta
>ap_chr3R_22997763_229977
taattc
>ap_chr3R_22997058_229970
tcatta
>ap_chr3R_22997200_229972
tgcttc
>ap_chr3R_22997018_229970
caattg
>ap_chr3R_22997214_229972
ttgtta
>ap_chr3R_22997008_229970
ttattt
>ap_chr3R_22997753_229977
atatta
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.370|c:0.130|g:0.130|t:0.370
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/ap_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	14
;	meme.llr                     	50
;	meme.E-value                 	2.3
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.13
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	2.89067
;	information.per.column       	0.481778
;	max.possible.info.per.col    	2.04022
;	consensus.strict             	tgattg
;	consensus.strict.rc          	caatca
;	consensus.IUPAC              	tgattv
;	consensus.IUPAC.rc           	baatca
;	consensus.regexp             	tgatt[acg]
;	consensus.regexp.rc          	[cgt]aatca
;	residues.content.crude.freq  	a:0.2857|c:0.0595|g:0.1071|t:0.5476
;	G+C.content.crude.freq       	0.166667
;	residues.content.corrected.freq	a:0.2913|c:0.0642|g:0.1087|t:0.5358
;	G+C.content.corrected.freq   	0.172889
;	min(P(S|M))                  	1.1048e-10
;	max(P(S|M))                  	0.109786
;	proba_range                  	0.109786
;	Wmin                         	-12.7
;	Wmax                         	5.3
;	Wrange                       	18
; Job started 2007_12_10.132032
; Job done    2007_12_10.132032