RegulonDB

CsgD matrix and aligment

matrix-quality result

Command: 
CsgD.2nt_upstream-noorf-ovlp-2str.17.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 CsgD.2nt_upstream-noorf-ovlp-2str.17.meme_quality_logo
; Input files
;	input	CsgD.2nt_upstream-noorf-ovlp-2str.17.meme_quality_matrix.tf
;	prior	CsgD.2nt_upstream-noorf-ovlp-2str.17.meme_quality2nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	CsgD.2nt_upstream-noorf-ovlp-2str.17.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	0	2	15	2	12	4	5	7	5	9	4	6	4	8	1	4	4
C	3	10	2	0	4	0	3	0	3	8	14	11	13	3	3	0	6
G	5	4	6	8	5	3	7	1	4	4	3	4	3	3	0	3	0
T	16	8	1	14	3	17	9	16	12	3	3	3	4	10	20	17	14
//
a  0.0  0.1  0.6  0.1  0.5  0.2  0.2  0.3  0.2  0.4  0.2  0.3  0.2  0.3  0.1  0.2  0.2
c  0.1  0.4  0.1  0.0  0.2  0.0  0.1  0.0  0.1  0.3  0.6  0.4  0.5  0.1  0.1  0.0  0.2
g  0.2  0.2  0.2  0.3  0.2  0.1  0.3  0.0  0.2  0.2  0.1  0.2  0.1  0.1  0.0  0.1  0.0
t  0.7  0.3  0.1  0.6  0.1  0.7  0.4  0.7  0.5  0.1  0.1  0.1  0.2  0.4  0.8  0.7  0.6
//
a -3.2 -1.2  0.7 -1.2  0.5 -0.5 -0.3  0.0 -0.3  0.2 -0.5 -0.1 -0.5  0.1 -1.7 -0.5 -0.5
c -0.5  0.7 -0.9 -3.2 -0.2 -3.2 -0.5 -3.2 -0.5  0.5  1.0  0.8  0.9 -0.5 -0.5 -3.2  0.2
g  0.0 -0.2  0.2  0.5  0.0 -0.5  0.3 -1.4 -0.2 -0.2 -0.5 -0.2 -0.5 -0.5 -3.2 -0.5 -3.2
t  0.8  0.1 -1.7  0.7 -0.8  0.8  0.2  0.8  0.5 -0.8 -0.8 -0.8 -0.5  0.3  1.0  0.8  0.7
//
a -0.0 -0.1  0.5 -0.1  0.3 -0.1 -0.1  0.0 -0.1  0.1 -0.1 -0.0 -0.1  0.0 -0.1 -0.1 -0.1
c -0.1  0.3 -0.1 -0.0 -0.0 -0.0 -0.1 -0.0 -0.1  0.1  0.6  0.3  0.5 -0.1 -0.1 -0.0  0.0
g  0.0 -0.0  0.0  0.2  0.0 -0.1  0.1 -0.1 -0.0 -0.0 -0.1 -0.0 -0.1 -0.1 -0.0 -0.1 -0.0
t  0.5  0.0 -0.1  0.4 -0.1  0.6  0.1  0.5  0.2 -0.1 -0.1 -0.1 -0.1  0.1  0.8  0.6  0.4
//
; Sites	
;
; Matrix parameters
;	Columns                      	17
;	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                  	kyrkrtkwtmCccwTty
;	min.prior                    	0.204759
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.65417
;	information.per.column       	0.273775
;	max.possible.info.per.col    	1.58592
;	consensus.strict             	tcatatgttcCcctTtt
;	consensus.strict.rc          	AAAAGGGGAACATATGA
;	consensus.IUPAC              	kyrkrtkwtmCccwTty
;	consensus.IUPAC.rc           	RAAWGGGKAWMAYMYRM
;	consensus.regexp             	[gt][ct][ag][gt][ag]t[gt][at]t[ac]Ccc[at]Tt[ct]
;	consensus.regexp.rc          	[AG]AA[AT]GGG[GT]A[AT][AC]A[CT][AC][CT][AG][AC]
;	residues.content.crude.freq  	a:0.2255|c:0.2034|g:0.1544|t:0.4167
;	G+C.content.crude.freq       	0.357843
;	residues.content.corrected.freq	a:0.2281|c:0.2036|g:0.1564|t:0.4119
;	G+C.content.corrected.freq   	0.360043
;	min(P(S|M))                  	1.4153e-24
;	max(P(S|M))                  	2.49835e-05
;	proba_range                  	2.49835e-05
;	Wmin                         	-30.7
;	Wmax                         	11.9
;	Wrange                       	42.6
; logo file:CsgD.2nt_upstream-noorf-ovlp-2str.17.meme_quality_logo_m1.png
; logo file:CsgD.2nt_upstream-noorf-ovlp-2str.17.meme_quality_logo_m1_rc.png
; Host name	compute-1-7.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.31
;	system	0.04
;	cuser	0.5
;	csystem	0.06
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