RegulonDB

CytR matrix and aligment

matrix-quality result

Command: 
CytR.1nt_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 CytR.1nt_upstream-noorf-ovlp-2str.18.meme_quality_logo
; Input files
;	input	CytR.1nt_upstream-noorf-ovlp-2str.18.meme_quality_matrix.tf
;	prior	CytR.1nt_upstream-noorf-ovlp-2str.18.meme_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	CytR.1nt_upstream-noorf-ovlp-2str.18.meme_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	11	3	11	6	6	2	1	0	1	17	5	5	12	13	10	10	3
C	10	5	9	1	4	1	0	3	1	14	0	1	2	3	3	2	0	4
G	1	1	3	3	3	3	2	2	10	3	1	0	6	0	0	1	5	2
T	0	1	3	3	5	8	14	12	7	0	0	12	5	3	2	5	3	9
//
a  0.4  0.6  0.2  0.6  0.3  0.3  0.1  0.1  0.0  0.1  0.9  0.3  0.3  0.6  0.7  0.5  0.5  0.2
c  0.5  0.3  0.5  0.1  0.2  0.1  0.0  0.2  0.1  0.7  0.0  0.1  0.1  0.2  0.2  0.1  0.0  0.2
g  0.1  0.1  0.2  0.2  0.2  0.2  0.1  0.1  0.5  0.2  0.1  0.0  0.3  0.0  0.0  0.1  0.3  0.1
t  0.0  0.1  0.2  0.2  0.3  0.4  0.8  0.6  0.4  0.0  0.0  0.6  0.3  0.2  0.1  0.3  0.2  0.5
//
a  0.3  0.7 -0.5  0.7  0.1  0.1 -0.9 -1.5 -2.9 -1.5  1.1 -0.0 -0.0  0.8  0.9  0.6  0.6 -0.5
c  0.9  0.3  0.8 -1.2  0.1 -1.2 -2.9 -0.2 -1.2  1.3 -2.9 -1.2 -0.6 -0.2 -0.2 -0.6 -2.9  0.1
g -1.2 -1.2 -0.2 -0.2 -0.2 -0.2 -0.6 -0.6  1.0 -0.2 -1.2 -2.9  0.5 -2.9 -2.9 -1.2  0.3 -0.6
t -2.9 -1.5 -0.5 -0.5 -0.1  0.4  0.9  0.8  0.3 -2.9 -2.9  0.8 -0.1 -0.5 -0.9 -0.1 -0.5  0.5
//
a  0.1  0.4 -0.1  0.4  0.0  0.0 -0.1 -0.1 -0.0 -0.1  1.0 -0.0 -0.0  0.5  0.6  0.3  0.3 -0.1
c  0.5  0.1  0.4 -0.1  0.0 -0.1 -0.0 -0.0 -0.1  1.0 -0.0 -0.1 -0.1 -0.0 -0.0 -0.1 -0.0  0.0
g -0.1 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.1  0.5 -0.0 -0.1 -0.0  0.2 -0.0 -0.0 -0.1  0.1 -0.1
t -0.0 -0.1 -0.1 -0.1 -0.0  0.2  0.7  0.5  0.1 -0.0 -0.0  0.5 -0.0 -0.1 -0.1 -0.0 -0.1  0.2
//
; Sites	
;
; Matrix parameters
;	Columns                      	18
;	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                    	1
;	AC                           	1
;	id                           	1
;	name                         	1
;	description                  	mmcamwttkCAtgaaary
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.12689
;	information.per.column       	0.340383
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	cacaatttgCAtgaaaat
;	consensus.strict.rc          	ATTTTCATGCAAATTGTG
;	consensus.IUPAC              	mmcamwttkCAtgaaary
;	consensus.IUPAC.rc           	RYTTTCATGMAAWKTGKK
;	consensus.regexp             	[ac][ac]ca[ac][at]tt[gt]CAtgaaa[ag][ct]
;	consensus.regexp.rc          	[AG][CT]TTTCATG[AC]AA[AT][GT]TG[GT][GT]
;	residues.content.crude.freq  	a:0.3796|c:0.1944|g:0.1420|t:0.2840
;	G+C.content.crude.freq       	0.33642
;	residues.content.corrected.freq	a:0.3749|c:0.1951|g:0.1453|t:0.2846
;	G+C.content.corrected.freq   	0.340437
;	min(P(S|M))                  	2.59287e-27
;	max(P(S|M))                  	3.2477e-05
;	proba_range                  	3.2477e-05
;	Wmin                         	-34.9
;	Wmax                         	13.6
;	Wrange                       	48.5
; logo file:CytR.1nt_upstream-noorf-ovlp-2str.18.meme_quality_logo_m1.png
; logo file:CytR.1nt_upstream-noorf-ovlp-2str.18.meme_quality_logo_m1_rc.png
; Host name	compute-1-3.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.31
;	system	0.04
;	cuser	0.51
;	csystem	0.05
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