RegulonDB

BasR matrix and aligment

matrix-quality result

Command: 
BasR.2nt_upstream-noorf-ovlp-2str.19.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 BasR.2nt_upstream-noorf-ovlp-2str.19.meme_quality_logo
; Input files
;	input	BasR.2nt_upstream-noorf-ovlp-2str.19.meme_quality_matrix.tf
;	prior	BasR.2nt_upstream-noorf-ovlp-2str.19.meme_quality2nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	BasR.2nt_upstream-noorf-ovlp-2str.19.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	0	6	6	0	4	6	6	5	1	1	0	0	8	8	0	2	1	1
C	0	2	2	2	1	1	0	2	1	5	5	0	0	0	0	0	1	0	0
G	0	1	0	0	3	1	0	0	0	0	1	0	0	0	0	6	4	3	2
T	8	5	0	0	4	2	2	0	2	2	1	8	8	0	0	2	1	4	5
//
a  0.0  0.0  0.7  0.7  0.0  0.5  0.7  0.7  0.6  0.1  0.1  0.0  0.0  0.9  0.9  0.0  0.3  0.1  0.1
c  0.0  0.2  0.2  0.2  0.1  0.1  0.0  0.2  0.1  0.6  0.6  0.0  0.0  0.0  0.0  0.0  0.1  0.0  0.0
g  0.0  0.1  0.0  0.0  0.4  0.1  0.0  0.0  0.0  0.0  0.1  0.0  0.0  0.0  0.0  0.7  0.5  0.4  0.2
t  0.9  0.6  0.0  0.0  0.5  0.3  0.3  0.0  0.3  0.3  0.1  0.9  0.9  0.0  0.0  0.3  0.1  0.5  0.6
//
a -2.2 -2.2  0.9  0.9 -2.2  0.5  0.9  0.9  0.7 -0.7 -0.7 -2.2 -2.2  1.2  1.2 -2.2 -0.1 -0.7 -0.7
c -2.2  0.2  0.2  0.2 -0.4 -0.4 -2.2  0.2 -0.4  1.0  1.0 -2.2 -2.2 -2.2 -2.2 -2.2 -0.4 -2.2 -2.2
g -2.2 -0.4 -2.2 -2.2  0.6 -0.4 -2.2 -2.2 -2.2 -2.2 -0.4 -2.2 -2.2 -2.2 -2.2  1.2  0.8  0.6  0.2
t  1.1  0.7 -2.2 -2.2  0.5 -0.1 -0.1 -2.2 -0.1 -0.1 -0.7  1.1  1.1 -2.2 -2.2 -0.1 -0.7  0.5  0.7
//
a -0.1 -0.1  0.6  0.6 -0.1  0.2  0.6  0.6  0.4 -0.1 -0.1 -0.1 -0.1  1.1  1.1 -0.1 -0.0 -0.1 -0.1
c -0.1  0.0  0.0  0.0 -0.1 -0.1 -0.1  0.0 -0.1  0.6  0.6 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
g -0.0 -0.1 -0.0 -0.0  0.2 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0  0.8  0.4  0.2  0.0
t  1.0  0.4 -0.1 -0.1  0.2 -0.0 -0.0 -0.1 -0.0 -0.0 -0.1  1.0  1.0 -0.1 -0.1 -0.0 -0.1  0.2  0.4
//
; Sites	
;
; Matrix parameters
;	Columns                      	19
;	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                  	TymmkaamaCCTTAAGgkk
;	min.prior                    	0.204759
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	9.59313
;	information.per.column       	0.504902
;	max.possible.info.per.col    	1.58592
;	consensus.strict             	TtaagaaaaCCTTAAGggt
;	consensus.strict.rc          	ACCCTTAAGGTTTTCTTAA
;	consensus.IUPAC              	TymmkaamaCCTTAAGgkk
;	consensus.IUPAC.rc           	MMCCTTAAGGTKTTMKKRA
;	consensus.regexp             	T[ct][ac][ac][gt]aa[ac]aCCTTAAGg[gt][gt]
;	consensus.regexp.rc          	[AC][AC]CCTTAAGGT[GT]TT[AC][GT][GT][AG]A
;	residues.content.crude.freq  	a:0.3618|c:0.1447|g:0.1382|t:0.3553
;	G+C.content.crude.freq       	0.282895
;	residues.content.corrected.freq	a:0.3540|c:0.1518|g:0.1456|t:0.3487
;	G+C.content.corrected.freq   	0.297334
;	min(P(S|M))                  	2.6247e-29
;	max(P(S|M))                  	0.000378537
;	proba_range                  	0.000378537
;	Wmin                         	-37.1
;	Wmax                         	17
;	Wrange                       	54.1
; logo file:BasR.2nt_upstream-noorf-ovlp-2str.19.meme_quality_logo_m1.png
; logo file:BasR.2nt_upstream-noorf-ovlp-2str.19.meme_quality_logo_m1_rc.png
; Host name	compute-1-10.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.31
;	system	0.05
;	cuser	0.49
;	csystem	0.06
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