; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/bcd.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/bcd_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/bcd.tab
; Output files
;	output	html_ready/bcd_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : bcd
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	8	45	46	1	0	3
c	|	3	1	0	0	45	27
g	|	1	1	2	13	1	3
t	|	36	1	0	34	2	15
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	48	48	48	48	48	48	288
; c.max	|	36	45	46	34	45	27	46
; c.min	|	1	1	0	0	0	3	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	8	3	1	36	|	48	 0.75	 0.43	t	t	ctttt
2	45	1	1	1	|	48	 0.94	 0.86	A	A	AAAAAAAAAAAt
3	46	0	2	0	|	48	 0.96	 0.96	A	A	AAAAAAAAAAAAAg
4	1	0	13	34	|	48	 0.71	 0.59	t	k	gttttt
5	0	45	1	2	|	48	 0.94	 1.27	C	C	CCCCCCCCCCCCCCCCg
6	3	27	3	15	|	48	 0.56	 0.42	C	Y	CCt
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.1  1.0  1.1 -0.1 -0.0 -0.1
c	| -0.1 -0.1 -0.0 -0.0  1.4  0.6
g	| -0.1 -0.1 -0.1  0.1 -0.1 -0.1
t	|  0.7 -0.1 -0.0  0.6 -0.1  0.0
;-	|-----|----|----|----|----|----|
; i.sum	|  0.4  0.9  1.0  0.6  1.3  0.4  4.5
; i.max	|  0.7  1.0  1.1  0.6  1.4  0.6  1.4
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	48
>bcd_chr2L_11455643_11455
taatcc
>bcd_chr2R_20730451_20730
taatcc
>bcd_chr3R_4520483_452049
taatcc
>bcd_chr3R_4520590_452060
taatcc
>bcd_chr2R_5489927_548993
taatcc
>bcd_chr3R_4522594_452261
taatcc
>bcd_chr2R_5489662_548967
taatcc
>bcd_chr3R_4520377_452038
taatcc
>bcd_chr2R_5490045_549005
taatcc
>bcd_chr2R_20730481_20730
taatcc
>bcd_chr3L_8639675_863968
taagcc
>bcd_chr2L_11455854_11455
taagcc
>bcd_chr2R_20730888_20730
taagcc
>bcd_chr3R_9720615_972062
taagcc
>bcd_chr2R_20730540_20730
taagcc
>bcd_chr3L_20631237_20631
taagcc
>bcd_chr3L_8641121_864113
taagcc
>bcd_chr3L_8640857_864086
taagcc
>bcd_chr3R_4522643_452265
taatct
>bcd_chr3R_26676912_26676
taatct
>bcd_chr3L_8639266_863927
taatct
>bcd_chr3L_20631195_20631
taatct
>bcd_chr3R_26676842_26676
taatct
>bcd_chr3R_26676964_26676
taatct
>bcd_chr2R_5489683_548969
taatct
>bcd_chr2L_11455773_11455
aaatcc
>bcd_chr3R_9720583_972059
aaatcc
>bcd_chr2L_11455823_11455
aaatcc
>bcd_chr2L_11455793_11455
aaatcc
>bcd_chr3R_4520539_452054
taagct
>bcd_chr3R_26676864_26676
taagct
>bcd_chr3R_4520555_452056
taagct
>bcd_chr3R_4520452_452046
caatcc
>bcd_chr2R_5489834_548984
taatcg
>bcd_chr3L_8639162_863917
caatct
>bcd_chr3R_26677097_26677
caatct
>bcd_chr3R_26676939_26676
gaatcc
>bcd_chr2L_11455737_11455
taagca
>bcd_chr3R_4520526_452053
tcatcc
>bcd_chr3L_8639430_863943
aaatcg
>bcd_chr3L_8639735_863974
tagtct
>bcd_chr3L_8639420_863942
ttagcc
>bcd_chr3R_4520506_452051
taattt
>bcd_chr3R_26677067_26677
taattt
>bcd_chr3R_26677189_26677
aaatgc
>bcd_chr3L_8639370_863937
tgatca
>bcd_chr3L_8641218_864122
aagtca
>bcd_chr2L_11456122_11456
aaaacg
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.306|c:0.194|g:0.194|t:0.306
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/bcd_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	48
;	meme.llr                     	230
;	meme.E-value                 	7.3e-32
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.194
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.52892
;	information.per.column       	0.754821
;	max.possible.info.per.col    	1.6399
;	consensus.strict             	tAAtCC
;	consensus.strict.rc          	GGaTTa
;	consensus.IUPAC              	tAAkCY
;	consensus.IUPAC.rc           	RGmTTa
;	consensus.regexp             	tAA[gt]C[CT]
;	consensus.regexp.rc          	[AG]G[ac]TTa
;	residues.content.crude.freq  	a:0.3576|c:0.2639|g:0.0729|t:0.3056
;	G+C.content.crude.freq       	0.336806
;	residues.content.corrected.freq	a:0.3566|c:0.2625|g:0.0754|t:0.3056
;	G+C.content.corrected.freq   	0.33785
;	min(P(S|M))                  	3.78872e-12
;	max(P(S|M))                  	0.232016
;	proba_range                  	0.232016
;	Wmin                         	-17.7
;	Wmax                         	6.7
;	Wrange                       	24.4
; Job started 2007_12_10.132034
; Job done    2007_12_10.132034