RegulonDB

GadE matrix and aligment

matrix-quality result

Command: 
GadE.2nt_upstream-noorf-ovlp-2str.18.meme_quality

Figures

Matrix logo

Decreasing cumulative distributions (dCDF)

Decreasing cumulative distributions (dCDF), logarithmic Y axis

ROC curve (logarithmic X axis)

Matrix information

; convert-matrix  -v 1 -from transfac -i GadE.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo
; Input files
;	input	GadE.2nt_upstream-noorf-ovlp-2str.18.meme_quality_matrix.tf
;	prior	GadE.2nt_upstream-noorf-ovlp-2str.18.meme_quality2nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	GadE.2nt_upstream-noorf-ovlp-2str.18.meme_quality_matrix_info.txt
; Output format       	tab
; pseudo-weight       	1
; Background model
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.29086
;		c	0.20809
;		g	0.20476
;		t	0.29629
A	4	0	0	3	1	1	1	2	2	3	0	5	1	0	2	5	5	2
C	0	1	1	0	0	0	0	1	0	0	0	0	0	1	0	0	0	2
G	1	4	4	0	0	2	0	0	1	0	0	0	1	0	2	0	0	0
T	0	0	0	2	4	2	4	2	2	2	5	0	3	4	1	0	0	1
//
a  0.7  0.0  0.0  0.5  0.2  0.2  0.2  0.4  0.4  0.5  0.0  0.9  0.2  0.0  0.4  0.9  0.9  0.4
c  0.0  0.2  0.2  0.0  0.0  0.0  0.0  0.2  0.0  0.0  0.0  0.0  0.0  0.2  0.0  0.0  0.0  0.4
g  0.2  0.7  0.7  0.0  0.0  0.4  0.0  0.0  0.2  0.0  0.0  0.0  0.2  0.0  0.4  0.0  0.0  0.0
t  0.0  0.0  0.0  0.4  0.7  0.4  0.7  0.4  0.4  0.4  0.9  0.0  0.5  0.7  0.2  0.0  0.0  0.2
//
a  0.9 -1.8 -1.8  0.6 -0.3 -0.3 -0.3  0.3  0.3  0.6 -1.8  1.1 -0.3 -1.8  0.3  1.1  1.1  0.3
c -1.8 -0.0 -0.0 -1.8 -1.8 -1.8 -1.8 -0.0 -1.8 -1.8 -1.8 -1.8 -1.8 -0.0 -1.8 -1.8 -1.8  0.6
g -0.0  1.2  1.2 -1.8 -1.8  0.6 -1.8 -1.8 -0.0 -1.8 -1.8 -1.8 -0.0 -1.8  0.6 -1.8 -1.8 -1.8
t -1.8 -1.8 -1.8  0.3  0.9  0.3  0.9  0.3  0.3  0.3  1.1 -1.8  0.6  0.9 -0.3 -1.8 -1.8 -0.3
//
a  0.6 -0.1 -0.1  0.3 -0.1 -0.1 -0.1  0.1  0.1  0.3 -0.1  1.0 -0.1 -0.1  0.1  1.0  1.0  0.1
c -0.1 -0.0 -0.0 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1  0.2
g -0.0  0.9  0.9 -0.1 -0.1  0.2 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.0 -0.1  0.2 -0.1 -0.1 -0.1
t -0.1 -0.1 -0.1  0.1  0.6  0.1  0.6  0.1  0.1  0.1  1.0 -0.1  0.3  0.6 -0.1 -0.1 -0.1 -0.1
//
; Sites	
;
; Matrix parameters
;	Columns                      	18
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.29085999082|c:0.208089935287|g:0.204758708047|t:0.296291365846
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	1
;	AC                           	1
;	id                           	1
;	name                         	1
;	description                  	aGGwtktwwwTAttrAAm
;	min.prior                    	0.204759
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	7.94803
;	information.per.column       	0.441557
;	max.possible.info.per.col    	1.58592
;	consensus.strict             	aGGatgtaaaTAttgAAc
;	consensus.strict.rc          	GTTCAATATTTACATCCT
;	consensus.IUPAC              	aGGwtktwwwTAttrAAm
;	consensus.IUPAC.rc           	KTTYAATAWWWAMAWCCT
;	consensus.regexp             	aGG[at]t[gt]t[at][at][at]TAtt[ag]AA[ac]
;	consensus.regexp.rc          	[GT]TT[CT]AATA[AT][AT][AT]A[AC]A[AT]CCT
;	residues.content.crude.freq  	a:0.4111|c:0.0667|g:0.1667|t:0.3556
;	G+C.content.crude.freq       	0.233333
;	residues.content.corrected.freq	a:0.3911|c:0.0902|g:0.1730|t:0.3457
;	G+C.content.corrected.freq   	0.263253
;	min(P(S|M))                  	8.62119e-27
;	max(P(S|M))                  	0.000105404
;	proba_range                  	0.000105404
;	Wmin                         	-32.3
;	Wmax                         	14.6
;	Wrange                       	46.9
; logo file:GadE.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo_m1.png
; logo file:GadE.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo_m1_rc.png
; Host name	compute-1-8.local
; Job started	2015-08-06.164357
; Job done	2015-08-06.164359
; Seconds	0.31
;	user	0.31
;	system	0.04
;	cuser	0.49
;	csystem	0.06
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