; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Mad.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Mad_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Mad.tab
; Output files
;	output	html_ready/Mad_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Mad
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7	8
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
a	|	4	1	11	0	2	4	0	13
c	|	12	0	5	19	0	10	16	0
g	|	2	18	0	0	15	5	3	6
t	|	1	0	3	0	2	0	0	0
; -----	|--------|-------|-------|-------|-------|-------|-------|-------|
; c.sum	|	19	19	19	19	19	19	19	19	152
; c.max	|	12	18	11	19	15	10	16	13	19
; c.min	|	1	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	4	12	2	1	|	19	 0.63	 0.24	c	m	ct
2	1	0	18	0	|	19	 0.95	 0.79	G	G	GGGGGGGGGG
3	11	5	0	3	|	19	 0.58	 0.56	A	A	AAct
4	0	19	0	0	|	19	 1.00	 0.93	C	C	CCCCCCCCCCCC
5	2	0	15	2	|	19	 0.79	 0.50	g	g	ggggt
6	4	10	5	0	|	19	 0.53	 0.19	c	m	c
7	0	16	3	0	|	19	 0.84	 0.57	c	c	cccccg
8	13	0	6	0	|	19	 0.68	 0.81	A	A	AAAAggg
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7    8
;-	|-----|----|----|----|----|----|----|----|
a	|  0.0 -0.1  0.7 -0.0 -0.0  0.0 -0.0  0.9
c	|  0.4 -0.0 -0.1  1.0 -0.0  0.2  0.7 -0.0
g	| -0.1  0.9 -0.0 -0.0  0.6 -0.1 -0.1 -0.0
t	| -0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0
;-	|-----|----|----|----|----|----|----|----|
; i.sum	|  0.2  0.8  0.6  0.9  0.5  0.2  0.6  0.8  4.6
; i.max	|  0.4  0.9  0.7  1.0  0.6  0.2  0.7  0.9  1.0
; i.min	| -0.1 -0.1 -0.1 -0.0 -0.0 -0.1 -0.1 -0.0 -0.1
; Sites	19
>Mad_chr3R_2579958_257997
agacgaca
>Mad_chr2R_8412650_841266
cgacggca
>Mad_chr2R_8412644_841266
cgacggca
>Mad_chr3R_2580283_258029
cgccgcca
>Mad_chr3R_2581266_258127
cgccgcca
>Mad_chr3R_2580310_258032
cgacaaca
>Mad_chr3R_17209435_17209
cgccgaca
>Mad_chr3R_17209509_17209
agactcca
>Mad_chr3R_21070780_21070
tgacgcca
>Mad_chr2L_13905216_13905
agacgcga
>Mad_chr3R_2580148_258016
caacgcca
>Mad_chr3R_17209467_17209
cgtcgccg
>Mad_chr3R_17209380_17209
cgtcgcga
>Mad_chr3R_2579983_257999
cgccgacg
>Mad_chr3R_2580464_258049
cgacgcgg
>Mad_chr3R_17209662_17209
cgacagcg
>Mad_chr2R_8412627_841263
ggccggca
>Mad_chr3R_2580333_258034
ggacggcg
>Mad_chr3R_2580045_258007
agtctccg
;
; Matrix parameters
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.167|c:0.333|g:0.333|t:0.167
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Mad_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	19
;	meme.llr                     	102
;	meme.E-value                 	2.3
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.167
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.58475
;	information.per.column       	0.573094
;	max.possible.info.per.col    	1.78976
;	consensus.strict             	cGACgccA
;	consensus.strict.rc          	TggcGTCg
;	consensus.IUPAC              	mGACgmcA
;	consensus.IUPAC.rc           	TgkcGTCk
;	consensus.regexp             	[ac]GACg[ac]cA
;	consensus.regexp.rc          	Tg[gt]cGTC[gt]
;	residues.content.crude.freq  	a:0.2303|c:0.4079|g:0.3224|t:0.0395
;	G+C.content.crude.freq       	0.730263
;	residues.content.corrected.freq	a:0.2271|c:0.4041|g:0.3229|t:0.0459
;	G+C.content.corrected.freq   	0.72705
;	min(P(S|M))                  	6.56601e-16
;	max(P(S|M))                  	0.0649687
;	proba_range                  	0.0649687
;	Wmin                         	-22.1
;	Wmax                         	7.5
;	Wrange                       	29.6
; Job started 2007_12_10.132114
; Job done    2007_12_10.132114