RegulonDB

DeoR matrix and aligment

matrix-quality result

Command: 
DeoR.1nt_upstream-noorf-ovlp-2str.19.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 DeoR.1nt_upstream-noorf-ovlp-2str.19.cons_quality_logo
; Input files
;	input	DeoR.1nt_upstream-noorf-ovlp-2str.19.cons_quality_matrix.tf
;	prior	DeoR.1nt_upstream-noorf-ovlp-2str.19.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	DeoR.1nt_upstream-noorf-ovlp-2str.19.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	6	1	0	1	1	4	1	3	5	0	3	0	0	3	7	0	7	4	6
C	1	0	1	3	1	0	2	4	0	0	0	3	2	4	0	6	0	2	1
G	0	0	5	0	0	1	3	0	0	2	0	2	0	0	0	1	0	1	0
T	0	6	1	3	5	2	1	0	2	5	4	2	5	0	0	0	0	0	0
//
a  0.8  0.2  0.0  0.2  0.2  0.5  0.2  0.4  0.7  0.0  0.4  0.0  0.0  0.4  0.9  0.0  0.9  0.5  0.8
c  0.2  0.0  0.2  0.4  0.2  0.0  0.3  0.5  0.0  0.0  0.0  0.4  0.3  0.5  0.0  0.8  0.0  0.3  0.2
g  0.0  0.0  0.7  0.0  0.0  0.2  0.4  0.0  0.0  0.3  0.0  0.3  0.0  0.0  0.0  0.2  0.0  0.2  0.0
t  0.0  0.8  0.2  0.4  0.7  0.3  0.2  0.0  0.3  0.7  0.5  0.3  0.7  0.0  0.0  0.0  0.0  0.0  0.0
//
a  1.0 -0.6 -2.1 -0.6 -0.6  0.6 -0.6  0.3  0.8 -2.1  0.3 -2.1 -2.1  0.3  1.1 -2.1  1.1  0.6  1.0
c -0.3 -2.1 -0.3  0.7 -0.3 -2.1  0.3  0.9 -2.1 -2.1 -2.1  0.7  0.3  0.9 -2.1  1.3 -2.1  0.3 -0.3
g -2.1 -2.1  1.2 -2.1 -2.1 -0.3  0.7 -2.1 -2.1  0.3 -2.1  0.3 -2.1 -2.1 -2.1 -0.3 -2.1 -0.3 -2.1
t -2.1  1.0 -0.6  0.3  0.8 -0.0 -0.6 -2.1 -0.0  0.8  0.6 -0.0  0.8 -2.1 -2.1 -2.1 -2.1 -2.1 -2.1
//
a  0.8 -0.1 -0.1 -0.1 -0.1  0.3 -0.1  0.1  0.5 -0.1  0.1 -0.1 -0.1  0.1  1.0 -0.1  1.0  0.3  0.8
c -0.0 -0.1 -0.0  0.3 -0.0 -0.1  0.1  0.5 -0.1 -0.1 -0.1  0.3  0.1  0.5 -0.1  1.0 -0.1  0.1 -0.0
g -0.1 -0.1  0.8 -0.1 -0.1 -0.0  0.3 -0.1 -0.1  0.1 -0.1  0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0 -0.1
t -0.1  0.8 -0.1  0.1  0.5 -0.0 -0.1 -0.1 -0.0  0.5  0.3 -0.0  0.5 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
//
; Sites	7
>site_0
ATGTAAGCAGAGTAACAAA
>site_1
ATCCCTTCTTTTTCACACA
>site_2
ATGATAAAATTTTCACAAA
>site_3
ATGTTAGAATTCTAACACA
>site_4
AATCTGCCTTACCCACAGC
>site_5
CTGCTTCCAGTGCCAGAAA
>site_6
ATGTTAGAATACTAACAAA
;
; Matrix parameters
;	Columns                      	19
;	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                    	DeoR.1nt_upstream-noorf-ovlp-2str.19.cons1
;	AC                           	DeoR.1nt_upstream-noorf-ovlp-2str.19.cons1
;	id                           	DeoR.1nt_upstream-noorf-ovlp-2str.19.cons1
;	name                         	DeoR.1nt_upstream-noorf-ovlp-2str.19.cons1
;	description                  	atGytasmakwsymACAma
;	statistical_basis            	7 sequences
;	sites                        	7
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	9.09172
;	information.per.column       	0.478512
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	atGctagcattctcACAaa
;	consensus.strict.rc          	TTTGTGAGAATGCTAGCAT
;	consensus.IUPAC              	atGytasmakwsymACAma
;	consensus.IUPAC.rc           	TKTGTKRSWMTKSTARCAT
;	consensus.regexp             	atG[ct]ta[cg][ac]a[gt][at][cg][ct][ac]ACA[ac]a
;	consensus.regexp.rc          	T[GT]TGT[GT][AG][CG][AT][AC]T[GT][CG]TA[AG]CAT
;	residues.content.crude.freq  	a:0.3910|c:0.2256|g:0.1128|t:0.2707
;	G+C.content.crude.freq       	0.338346
;	residues.content.corrected.freq	a:0.3784|c:0.2233|g:0.1243|t:0.2739
;	G+C.content.corrected.freq   	0.347647
;	min(P(S|M))                  	1.544e-29
;	max(P(S|M))                  	0.000110805
;	proba_range                  	0.000110805
;	Wmin                         	-38.1
;	Wmax                         	16.7
;	Wrange                       	54.8
; logo file:DeoR.1nt_upstream-noorf-ovlp-2str.19.cons_quality_logo_m1.png
; logo file:DeoR.1nt_upstream-noorf-ovlp-2str.19.cons_quality_logo_m1_rc.png
; Host name	compute-1-8.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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