RegulonDB

DnaA matrix and aligment

matrix-quality result

Command: 
DnaA.2nt_upstream-noorf-ovlp-2str.11.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 DnaA.2nt_upstream-noorf-ovlp-2str.11.meme_quality_logo
; Input files
;	input	DnaA.2nt_upstream-noorf-ovlp-2str.11.meme_quality_matrix.tf
;	prior	DnaA.2nt_upstream-noorf-ovlp-2str.11.meme_quality2nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	DnaA.2nt_upstream-noorf-ovlp-2str.11.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	7	3	2	1	10	0	0	1	13	0	13
C	1	1	1	0	0	1	9	13	1	12	0
G	3	5	0	0	0	0	1	0	0	2	0
T	3	5	11	13	4	13	4	0	0	0	1
//
a  0.5  0.2  0.2  0.1  0.7  0.0  0.0  0.1  0.9  0.0  0.9
c  0.1  0.1  0.1  0.0  0.0  0.1  0.6  0.9  0.1  0.8  0.0
g  0.2  0.3  0.0  0.0  0.0  0.0  0.1  0.0  0.0  0.1  0.0
t  0.2  0.4  0.8  0.9  0.3  0.9  0.3  0.0  0.0  0.0  0.1
//
a  0.5 -0.3 -0.6 -1.2  0.9 -2.7 -2.7 -1.2  1.1 -2.7  1.1
c -0.9 -0.9 -0.9 -2.7 -2.7 -0.9  1.1  1.4 -0.9  1.4 -2.7
g  0.0  0.5 -2.7 -2.7 -2.7 -2.7 -0.9 -2.7 -2.7 -0.3 -2.7
t -0.3  0.2  0.9  1.1 -0.0  1.1 -0.0 -2.7 -2.7 -2.7 -1.2
//
a  0.2 -0.1 -0.1 -0.1  0.6 -0.1 -0.1 -0.1  1.0 -0.1  1.0
c -0.1 -0.1 -0.1 -0.0 -0.0 -0.1  0.7  1.3 -0.1  1.1 -0.0
g  0.0  0.2 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0
t -0.1  0.1  0.7  1.0 -0.0  1.0 -0.0 -0.1 -0.1 -0.1 -0.1
//
; Sites	
;
; Matrix parameters
;	Columns                      	11
;	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                  	rktTaTCCACA
;	min.prior                    	0.204759
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.9989
;	information.per.column       	0.636263
;	max.possible.info.per.col    	1.58592
;	consensus.strict             	agtTaTCCACA
;	consensus.strict.rc          	TGTGGATAACT
;	consensus.IUPAC              	rktTaTCCACA
;	consensus.IUPAC.rc           	TGTGGATAAMY
;	consensus.regexp             	[ag][gt]tTaTCCACA
;	consensus.regexp.rc          	TGTGGATAA[AC][CT]
;	residues.content.crude.freq  	a:0.3247|c:0.2532|g:0.0714|t:0.3506
;	G+C.content.crude.freq       	0.324675
;	residues.content.corrected.freq	a:0.3224|c:0.2502|g:0.0803|t:0.3470
;	G+C.content.corrected.freq   	0.330554
;	min(P(S|M))                  	2.15407e-19
;	max(P(S|M))                  	0.0240635
;	proba_range                  	0.0240635
;	Wmin                         	-26.3
;	Wmax                         	11.2
;	Wrange                       	37.5
; logo file:DnaA.2nt_upstream-noorf-ovlp-2str.11.meme_quality_logo_m1.png
; logo file:DnaA.2nt_upstream-noorf-ovlp-2str.11.meme_quality_logo_m1_rc.png
; Host name	compute-1-9.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.32
;	system	0.04
;	cuser	0.48
;	csystem	0.06
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