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GcvA matrix and aligment

matrix-quality result

Command: 
GcvA.1nt_upstream-noorf-ovlp-2str.11.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 GcvA.1nt_upstream-noorf-ovlp-2str.11.cons_quality_logo
; Input files
;	input	GcvA.1nt_upstream-noorf-ovlp-2str.11.cons_quality_matrix.tf
;	prior	GcvA.1nt_upstream-noorf-ovlp-2str.11.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	GcvA.1nt_upstream-noorf-ovlp-2str.11.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	0	6	0	3	4	0	4	4	6	4	3
C	6	0	0	0	0	0	1	0	0	0	0
G	0	0	1	0	0	4	1	0	0	0	0
T	0	0	5	3	2	2	0	2	0	2	3
//
a  0.0  0.9  0.0  0.5  0.6  0.0  0.6  0.6  0.9  0.6  0.5
c  0.9  0.0  0.0  0.0  0.0  0.0  0.2  0.0  0.0  0.0  0.0
g  0.0  0.0  0.2  0.0  0.0  0.6  0.2  0.0  0.0  0.0  0.0
t  0.0  0.0  0.8  0.5  0.3  0.3  0.0  0.3  0.0  0.3  0.5
//
a -1.9  1.1 -1.9  0.5  0.7 -1.9  0.7  0.7  1.1  0.7  0.5
c  1.5 -1.9 -1.9 -1.9 -1.9 -1.9 -0.2 -1.9 -1.9 -1.9 -1.9
g -1.9 -1.9 -0.2 -1.9 -1.9  1.1 -0.2 -1.9 -1.9 -1.9 -1.9
t -1.9 -1.9  0.9  0.5  0.1  0.1 -1.9  0.1 -1.9  0.1  0.5
//
a -0.1  1.0 -0.1  0.2  0.5 -0.1  0.5  0.5  1.0  0.5  0.2
c  1.3 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1
g -0.1 -0.1 -0.0 -0.1 -0.1  0.6 -0.0 -0.1 -0.1 -0.1 -0.1
t -0.1 -0.1  0.7  0.2  0.0  0.0 -0.1  0.0 -0.1  0.0  0.2
//
; Sites	6
>site_0
CAGATTAAAAA
>site_1
CATTATAAATT
>site_2
CATAAGGTAAA
>site_3
CATAAGCTAAT
>site_4
CATTAGAAAAT
>site_5
CATTTGAAATA
;
; Matrix parameters
;	Columns                      	11
;	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                    	GcvA.1nt_upstream-noorf-ovlp-2str.11.cons1
;	AC                           	GcvA.1nt_upstream-noorf-ovlp-2str.11.cons1
;	id                           	GcvA.1nt_upstream-noorf-ovlp-2str.11.cons1
;	name                         	GcvA.1nt_upstream-noorf-ovlp-2str.11.cons1
;	description                  	CAtwwKawAww
;	statistical_basis            	6 sequences
;	sites                        	6
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.87972
;	information.per.column       	0.53452
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	CAtaaGaaAaa
;	consensus.strict.rc          	TTTTTCTTATG
;	consensus.IUPAC              	CAtwwKawAww
;	consensus.IUPAC.rc           	WWTWTMWWATG
;	consensus.regexp             	CAt[at][at][GT]a[at]A[at][at]
;	consensus.regexp.rc          	[AT][AT]T[AT]T[AC][AT][AT]ATG
;	residues.content.crude.freq  	a:0.5152|c:0.1061|g:0.0909|t:0.2879
;	G+C.content.crude.freq       	0.19697
;	residues.content.corrected.freq	a:0.4831|c:0.1206|g:0.1072|t:0.2891
;	G+C.content.corrected.freq   	0.227796
;	min(P(S|M))                  	2.01446e-17
;	max(P(S|M))                  	0.0101913
;	proba_range                  	0.0101913
;	Wmin                         	-21.5
;	Wmax                         	9.7
;	Wrange                       	31.2
; logo file:GcvA.1nt_upstream-noorf-ovlp-2str.11.cons_quality_logo_m1.png
; logo file:GcvA.1nt_upstream-noorf-ovlp-2str.11.cons_quality_logo_m1_rc.png
; Host name	compute-1-10.local
; Job started	2015-08-06.164357
; Job done	2015-08-06.164359
; Seconds	0.31
;	user	0.31
;	system	0.05
;	cuser	0.49
;	csystem	0.05
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