RegulonDB

BaeR matrix and aligment

matrix-quality result

Command: 
BaeR.1nt_upstream-noorf-ovlp-2str.18.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 BaeR.1nt_upstream-noorf-ovlp-2str.18.cons_quality_logo
; Input files
;	input	BaeR.1nt_upstream-noorf-ovlp-2str.18.cons_quality_matrix.tf
;	prior	BaeR.1nt_upstream-noorf-ovlp-2str.18.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	BaeR.1nt_upstream-noorf-ovlp-2str.18.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	0	1	0	0	0	0	0	0	0	3	0	2	4	0	0	0	0	0
C	0	0	0	0	0	4	0	3	4	1	1	0	0	0	1	0	1	3
G	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	3	3	0
T	4	3	3	4	4	0	4	1	0	0	3	1	0	4	3	1	0	1
//
a  0.1  0.3  0.1  0.1  0.1  0.1  0.1  0.1  0.1  0.7  0.1  0.5  0.9  0.1  0.1  0.1  0.1  0.1
c  0.0  0.0  0.0  0.0  0.0  0.8  0.0  0.6  0.8  0.2  0.2  0.0  0.0  0.0  0.2  0.0  0.2  0.6
g  0.0  0.0  0.2  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.2  0.0  0.0  0.0  0.6  0.6  0.0
t  0.9  0.7  0.7  0.9  0.9  0.1  0.9  0.3  0.1  0.1  0.7  0.3  0.1  0.9  0.7  0.3  0.1  0.3
//
a -1.6 -0.1 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6  0.8 -1.6  0.5  1.1 -1.6 -1.6 -1.6 -1.6 -1.6
c -1.6 -1.6 -1.6 -1.6 -1.6  1.4 -1.6  1.1  1.4  0.2  0.2 -1.6 -1.6 -1.6  0.2 -1.6  0.2  1.1
g -1.6 -1.6  0.2 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6  0.2 -1.6 -1.6 -1.6  1.1  1.1 -1.6
t  1.1  0.8  0.8  1.1  1.1 -1.6  1.1 -0.1 -1.6 -1.6  0.8 -0.1 -1.6  1.1  0.8 -0.1 -1.6 -0.1
//
a -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  0.5 -0.1  0.2  0.9 -0.1 -0.1 -0.1 -0.1 -0.1
c -0.1 -0.1 -0.1 -0.1 -0.1  1.2 -0.1  0.7  1.2  0.0  0.0 -0.1 -0.1 -0.1  0.0 -0.1  0.0  0.7
g -0.1 -0.1  0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  0.0 -0.1 -0.1 -0.1  0.7  0.7 -0.1
t  0.9  0.5  0.5  0.9  0.9 -0.1  0.9 -0.0 -0.1 -0.1  0.5 -0.0 -0.1  0.9  0.5 -0.0 -0.1 -0.0
//
; Sites	4
>site_0
TTTTTCTCCATAATTGGC
>site_1
TAGTTCTTCATAATCTCT
>site_2
TTTTTCTCCCTTATTGGC
>site_3
TTTTTCTCCACGATTGGC
;
; 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                    	BaeR.1nt_upstream-noorf-ovlp-2str.18.cons1
;	AC                           	BaeR.1nt_upstream-noorf-ovlp-2str.18.cons1
;	id                           	BaeR.1nt_upstream-noorf-ovlp-2str.18.cons1
;	name                         	BaeR.1nt_upstream-noorf-ovlp-2str.18.cons1
;	description                  	TtkTTCTCCmyrATyGSC
;	statistical_basis            	4 sequences
;	sites                        	4
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	10.2885
;	information.per.column       	0.571583
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	TttTTCTCCataATtGGC
;	consensus.strict.rc          	GCCAATTATGGAGAAAAA
;	consensus.IUPAC              	TtkTTCTCCmyrATyGSC
;	consensus.IUPAC.rc           	GSCRATYRKGGAGAAMAA
;	consensus.regexp             	Tt[gt]TTCTCC[ac][ct][ag]AT[ct]G[CG]C
;	consensus.regexp.rc          	G[CG]C[AG]AT[CT][AG][GT]GGAGAA[AC]AA
;	residues.content.crude.freq  	a:0.1389|c:0.2500|g:0.1111|t:0.5000
;	G+C.content.crude.freq       	0.361111
;	residues.content.corrected.freq	a:0.1692|c:0.2416|g:0.1299|t:0.4593
;	G+C.content.corrected.freq   	0.371439
;	min(P(S|M))                  	1.57429e-25
;	max(P(S|M))                  	0.00274397
;	proba_range                  	0.00274397
;	Wmin                         	-29
;	Wmax                         	18.3
;	Wrange                       	47.3
; logo file:BaeR.1nt_upstream-noorf-ovlp-2str.18.cons_quality_logo_m1.png
; logo file:BaeR.1nt_upstream-noorf-ovlp-2str.18.cons_quality_logo_m1_rc.png
; Host name	compute-1-2.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.31
;	system	0.05
;	cuser	0.5
;	csystem	0.05
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