RegulonDB

CpxR matrix and aligment

matrix-quality result

Command: 
CpxR.1nt_upstream-noorf-ovlp-2str.14.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 CpxR.1nt_upstream-noorf-ovlp-2str.14.cons_quality_logo
; Input files
;	input	CpxR.1nt_upstream-noorf-ovlp-2str.14.cons_quality_matrix.tf
;	prior	CpxR.1nt_upstream-noorf-ovlp-2str.14.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	CpxR.1nt_upstream-noorf-ovlp-2str.14.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	8	35	0	20	11	20	14	13	9	9	1	41	11
C	2	0	0	40	11	17	8	2	15	8	0	1	1	45
G	2	11	7	4	19	8	8	15	7	9	0	6	7	2
T	48	39	16	14	8	22	22	27	23	32	49	50	9	0
//
a  0.1  0.1  0.6  0.0  0.3  0.2  0.3  0.2  0.2  0.2  0.2  0.0  0.7  0.2
c  0.0  0.0  0.0  0.7  0.2  0.3  0.1  0.0  0.3  0.1  0.0  0.0  0.0  0.8
g  0.0  0.2  0.1  0.1  0.3  0.1  0.1  0.3  0.1  0.2  0.0  0.1  0.1  0.0
t  0.8  0.7  0.3  0.2  0.1  0.4  0.4  0.5  0.4  0.5  0.8  0.9  0.2  0.0
//
a -1.0 -0.7  0.7 -4.1  0.2 -0.4  0.2 -0.2 -0.3 -0.6 -0.6 -2.6  0.9 -0.4
c -1.7 -4.1 -4.1  1.2 -0.1  0.3 -0.4 -1.7  0.2 -0.4 -4.1 -2.3 -2.3  1.3
g -1.7 -0.1 -0.5 -1.1  0.5 -0.4 -0.4  0.2 -0.5 -0.3 -4.1 -0.7 -0.5 -1.7
t  1.0  0.8 -0.1 -0.2 -0.7  0.2  0.2  0.4  0.3  0.6  1.0  1.1 -0.6 -4.1
//
a -0.1 -0.1  0.4 -0.0  0.1 -0.1  0.1 -0.0 -0.1 -0.1 -0.1 -0.1  0.6 -0.1
c -0.1 -0.0 -0.0  0.8 -0.0  0.1 -0.1 -0.1  0.1 -0.1 -0.0 -0.0 -0.0  1.0
g -0.1 -0.0 -0.1 -0.1  0.2 -0.1 -0.1  0.1 -0.1 -0.0 -0.0 -0.1 -0.1 -0.1
t  0.8  0.5 -0.0 -0.0 -0.1  0.1  0.1  0.2  0.1  0.3  0.9  0.9 -0.1 -0.0
//
; Sites	58
>site_0
TGACGGTAATTTAC
>site_1
TTGTTCGTCTTTAC
>site_2
TTACCAGGTTTTAC
>site_3
GGTGATCTCTTTAC
>site_4
TTTCAGTGCTTTAC
>site_5
CAACGCTTAGTTTA
>site_6
TTACGAAAAATTAC
>site_7
AAACGGGGTTTTAC
>site_8
TTTTTCTTTTTGAA
>site_9
TTACTTTTGGTTAC
>site_10
TTACGGAATATTAC
>site_11
TATCTGTTTGTTAA
>site_12
TTACCCATCTTTAC
>site_13
TTTTATAAACATTC
>site_14
TTACATCTGATTTC
>site_15
TTACAAATCTTAAA
>site_16
AGTTACATGTTTAA
>site_17
TATTAAAATGTTAA
>site_18
TTTTATTAAGTTTA
>site_19
TTTTCTATCATTTC
>site_20
TTGGTTTTTATTGC
>site_21
TTGCACAATTTTAA
>site_22
TGGTGATAACTTAC
>site_23
ATATGCATTATTAG
>site_24
GGACAATTTTTTAC
>site_25
TAACGCTGCGTTAC
>site_26
TTACAAATTCTTTG
>site_27
TGACTTATACTTGC
>site_28
TTTCATAGAAATCC
>site_29
TTTCATTGTTTTAC
>site_30
TTGTCTCGATATAC
>site_31
TTACGTCTTTTTAC
>site_32
TTATATATTTTTAC
>site_33
TAACGCGTAGATAA
>site_34
AGACGATTCCAGAC
>site_35
ATTTACATTTTGAA
>site_36
TTATTTCGCCATTC
>site_37
TTACCCTTCTTTAC
>site_38
TTACATTAACTGAC
>site_39
TGACCAAAGAATAC
>site_40
ATGCCCTTTTATAC
>site_41
TTACGGAACTTTAC
>site_42
TTACATTTTTTTGC
>site_43
TTACGGCGTTTTGC
>site_44
TTAGGTGAAGAGGC
>site_45
TTTGTTGCCTTTAC
>site_46
TTTCGCCGCTTTAC
>site_47
TTACACAGGCTGAC
>site_48
TTACCTAATTTTAC
>site_49
CGGTAATGGTTTTC
>site_50
TGACCGTTTGTTTA
>site_51
TATCCCCGCTTTAC
>site_52
TTACAAGCTTTTAC
>site_53
TTACGTTGTTTTAC
>site_54
TGACGCATGTTTGC
>site_55
TATCGTTGAATCGC
>site_56
TTACGCGTTTTTAC
>site_57
TTACCTTACTTTAC
;
; Matrix parameters
;	Columns                      	14
;	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                    	CpxR.1nt_upstream-noorf-ovlp-2str.14.cons1
;	AC                           	CpxR.1nt_upstream-noorf-ovlp-2str.14.cons1
;	id                           	CpxR.1nt_upstream-noorf-ovlp-2str.14.cons1
;	name                         	CpxR.1nt_upstream-noorf-ovlp-2str.14.cons1
;	description                  	TtaCrywkytTTaC
;	statistical_basis            	58 sequences
;	sites                        	58
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.23746
;	information.per.column       	0.374104
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	TtaCgcttttTTaC
;	consensus.strict.rc          	GTAAAAAAGCGTAA
;	consensus.IUPAC              	TtaCrywkytTTaC
;	consensus.IUPAC.rc           	GTAAARMWRYGTAA
;	consensus.regexp             	TtaC[ag][ct][at][gt][ct]tTTaC
;	consensus.regexp.rc          	GTAAA[AG][AC][AT][AG][CT]GTAA
;	residues.content.crude.freq  	a:0.2438|c:0.1847|g:0.1293|t:0.4421
;	G+C.content.crude.freq       	0.314039
;	residues.content.corrected.freq	a:0.2446|c:0.1851|g:0.1306|t:0.4397
;	G+C.content.corrected.freq   	0.315712
;	min(P(S|M))                  	2.89007e-23
;	max(P(S|M))                  	0.000416934
;	proba_range                  	0.000416934
;	Wmin                         	-31.5
;	Wmax                         	10.4
;	Wrange                       	41.9
; logo file:CpxR.1nt_upstream-noorf-ovlp-2str.14.cons_quality_logo_m1.png
; logo file:CpxR.1nt_upstream-noorf-ovlp-2str.14.cons_quality_logo_m1_rc.png
; Host name	compute-1-0.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.3
;	user	0.3
;	system	0.05
;	cuser	0.51
;	csystem	0.05
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