RegulonDB

ExuR matrix and aligment

matrix-quality result

Command: 
ExuR.1nt_upstream-noorf-ovlp-2str.17.cons_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 ExuR.1nt_upstream-noorf-ovlp-2str.17.cons_quality_logo
; Input files
;	input	ExuR.1nt_upstream-noorf-ovlp-2str.17.cons_quality_matrix.tf
;	prior	ExuR.1nt_upstream-noorf-ovlp-2str.17.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	ExuR.1nt_upstream-noorf-ovlp-2str.17.cons_quality_matrix_info.txt
; Output format       	tab
; pseudo-weight       	1
; Background model
;	Bernoulli model (order=0)
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.29063
;		c	0.20784
;		g	0.20492
;		t	0.29662
A	7	1	1	1	0	1	0	2	2	9	0	2	9	2	0	0	0
C	1	2	0	0	0	0	1	1	0	0	8	6	0	6	0	0	0
G	1	0	3	1	8	3	1	0	3	0	0	0	0	1	1	0	0
T	0	6	5	7	1	5	7	6	4	0	1	1	0	0	8	9	9
//
a  0.7  0.1  0.1  0.1  0.0  0.1  0.0  0.2  0.2  0.9  0.0  0.2  0.9  0.2  0.0  0.0  0.0
c  0.1  0.2  0.0  0.0  0.0  0.0  0.1  0.1  0.0  0.0  0.8  0.6  0.0  0.6  0.0  0.0  0.0
g  0.1  0.0  0.3  0.1  0.8  0.3  0.1  0.0  0.3  0.0  0.0  0.0  0.0  0.1  0.1  0.0  0.0
t  0.0  0.6  0.5  0.7  0.1  0.5  0.7  0.6  0.4  0.0  0.1  0.1  0.0  0.0  0.8  0.9  0.9
//
a  0.9 -0.8 -0.8 -0.8 -2.3 -0.8 -2.3 -0.2 -0.2  1.2 -2.3 -0.2  1.2 -0.2 -2.3 -2.3 -2.3
c -0.5  0.1 -2.3 -2.3 -2.3 -2.3 -0.5 -0.5 -2.3 -2.3  1.4  1.1 -2.3  1.1 -2.3 -2.3 -2.3
g -0.5 -2.3  0.4 -0.5  1.4  0.4 -0.5 -2.3  0.4 -2.3 -2.3 -2.3 -2.3 -0.5 -0.5 -2.3 -2.3
t -2.3  0.8  0.6  0.9 -0.8  0.6  0.9  0.8  0.4 -2.3 -0.8 -0.8 -2.3 -2.3  1.0  1.1  1.1
//
a  0.7 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  1.1 -0.1 -0.1  1.1 -0.1 -0.1 -0.1 -0.1
c -0.1  0.0 -0.0 -0.0 -0.0 -0.0 -0.1 -0.1 -0.0 -0.0  1.1  0.7 -0.0  0.7 -0.0 -0.0 -0.0
g -0.1 -0.0  0.1 -0.1  1.1  0.1 -0.1 -0.0  0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.1 -0.0 -0.0
t -0.1  0.5  0.3  0.7 -0.1  0.3  0.7  0.5  0.2 -0.1 -0.1 -0.1 -0.1 -0.1  0.9  1.1  1.1
//
; Sites	9
>site_0
ATGTGTTCTACCACTTT
>site_1
ATTGGTGTGATAACTTT
>site_2
ATTTTTTTAACTACGTT
>site_3
GCGAGATTTACCACTTT
>site_4
ACTTGTCATACAACTTT
>site_5
ATTTGTTATACCACTTT
>site_6
CAATGGTTGACCAATTT
>site_7
ATGTGGTTAACCAATTT
>site_8
ATTTGGTTGACCAGTTT
;
; Matrix parameters
;	Columns                      	17
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.2906296|c:0.2078359|g:0.2049154|t:0.2966191
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	ExuR.1nt_upstream-noorf-ovlp-2str.17.cons1
;	AC                           	ExuR.1nt_upstream-noorf-ovlp-2str.17.cons1
;	id                           	ExuR.1nt_upstream-noorf-ovlp-2str.17.cons1
;	name                         	ExuR.1nt_upstream-noorf-ovlp-2str.17.cons1
;	description                  	ayktGkttkACCACTTT
;	statistical_basis            	9 sequences
;	sites                        	9
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	9.90339
;	information.per.column       	0.582552
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	atttGtttgACCACTTT
;	consensus.strict.rc          	AAAGTGGTCAAACAAAT
;	consensus.IUPAC              	ayktGkttkACCACTTT
;	consensus.IUPAC.rc           	AAAGTGGTMAAMCAMRT
;	consensus.regexp             	a[ct][gt]tG[gt]tt[gt]ACCACTTT
;	consensus.regexp.rc          	AAAGTGGT[AC]AA[AC]CA[AC][AG]T
;	residues.content.crude.freq  	a:0.2418|c:0.1634|g:0.1438|t:0.4510
;	G+C.content.crude.freq       	0.30719
;	residues.content.corrected.freq	a:0.2467|c:0.1678|g:0.1499|t:0.4355
;	G+C.content.corrected.freq   	0.317746
;	min(P(S|M))                  	6.40705e-29
;	max(P(S|M))                  	0.0029797
;	proba_range                  	0.0029797
;	Wmin                         	-39.2
;	Wmax                         	16.5
;	Wrange                       	55.7
; logo file:ExuR.1nt_upstream-noorf-ovlp-2str.17.cons_quality_logo_m1.png
; logo file:ExuR.1nt_upstream-noorf-ovlp-2str.17.cons_quality_logo_m1_rc.png
; Host name	compute-1-5.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.32
;	user	0.32
;	system	0.04
;	cuser	0.51
;	csystem	0.06
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