RegulonDB

Cra matrix and aligment

matrix-quality result

Command: 
Cra.1nt_upstream-noorf-ovlp-2str.16.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 Cra.1nt_upstream-noorf-ovlp-2str.16.cons_quality_logo
; Input files
;	input	Cra.1nt_upstream-noorf-ovlp-2str.16.cons_quality_matrix.tf
;	prior	Cra.1nt_upstream-noorf-ovlp-2str.16.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	Cra.1nt_upstream-noorf-ovlp-2str.16.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	22	6	7	4	28	34	17	1	7	28	2	0	2	33	1	5
C	6	14	5	0	0	6	6	37	2	3	0	2	32	4	6	33
G	12	5	1	24	5	0	6	2	33	0	0	0	0	0	32	0
T	2	17	29	14	9	2	13	2	0	11	40	40	8	5	3	4
//
a  0.5  0.1  0.2  0.1  0.7  0.8  0.4  0.0  0.2  0.7  0.1  0.0  0.1  0.8  0.0  0.1
c  0.1  0.3  0.1  0.0  0.0  0.1  0.1  0.9  0.1  0.1  0.0  0.1  0.7  0.1  0.1  0.8
g  0.3  0.1  0.0  0.6  0.1  0.0  0.1  0.1  0.8  0.0  0.0  0.0  0.0  0.0  0.7  0.0
t  0.1  0.4  0.7  0.3  0.2  0.1  0.3  0.1  0.0  0.3  0.9  0.9  0.2  0.1  0.1  0.1
//
a  0.6 -0.7 -0.5 -1.1  0.8  1.0  0.3 -2.3 -0.5  0.8 -1.7 -3.8 -1.7  1.0 -2.3 -0.9
c -0.4  0.5 -0.5 -3.8 -3.8 -0.4 -0.4  1.4 -1.4 -1.0 -3.8 -1.4  1.3 -0.8 -0.4  1.3
g  0.3 -0.5 -2.0  1.0 -0.5 -3.8 -0.4 -1.4  1.3 -3.8 -3.8 -3.8 -3.8 -3.8  1.3 -3.8
t -1.7  0.3  0.8  0.1 -0.3 -1.7  0.0 -1.7 -3.8 -0.1  1.2  1.2 -0.4 -0.9 -1.4 -1.1
//
a  0.3 -0.1 -0.1 -0.1  0.5  0.8  0.1 -0.1 -0.1  0.5 -0.1 -0.0 -0.1  0.8 -0.1 -0.1
c -0.1  0.2 -0.1 -0.0 -0.0 -0.1 -0.1  1.2 -0.1 -0.1 -0.0 -0.1  1.0 -0.1 -0.1  1.0
g  0.1 -0.1 -0.1  0.6 -0.1 -0.0 -0.1 -0.1  1.0 -0.0 -0.0 -0.0 -0.0 -0.0  1.0 -0.0
t -0.1  0.1  0.6  0.0 -0.1 -0.1  0.0 -0.1 -0.0 -0.0  1.1  1.1 -0.1 -0.1 -0.1 -0.1
//
; Sites	42
>site_0
ATCGATACGATCCTGC
>site_1
ATTGAACCGATTCACT
>site_2
ACTGAATCCATTCAGC
>site_3
AATTTAACAATCCAGA
>site_4
AAATATGCGTTTCAGT
>site_5
TCTTACACGATTCAGC
>site_6
GTTGAAGCAAATTTGC
>site_7
ATTGTAAGGATTTTGC
>site_8
GTAGTAATAAATCAGC
>site_9
ACCGAAATATTTTTTA
>site_10
ACAAGAACGTTTTACA
>site_11
ATTAAATCATTTCAAC
>site_12
GGTTAAGCGATTCAGC
>site_13
GCTGACACCTTTCAGC
>site_14
CTTGAACCGATTTAGC
>site_15
CTTGAATGGTTTCAGC
>site_16
GCTTGAACGATTCACC
>site_17
GAAAAAACGATTCAGC
>site_18
ATTGACACGATTCCGC
>site_19
ATCGAATCGATTCAGA
>site_20
ACTGAAACGTTTTTGC
>site_21
CGTTTACAGTTTTCGC
>site_22
GTTGGCTCGATTCATC
>site_23
ATTGAAACGATTCAGC
>site_24
CTTGAAACGTTTCAGC
>site_25
ACTTTATCGTTTCAGC
>site_26
ATAAAATCGATTCAGC
>site_27
GATGAACCGTTTCATC
>site_28
AACTGATCGATTCACA
>site_29
TTGTAAACGATTCAGC
>site_30
ACTGAAACGCTTCAGC
>site_31
ACATAATCACTTACGT
>site_32
GGTGTCTCGCTTCAGC
>site_33
ACCTTAACGATTCAGC
>site_34
AAAGTATCGATTCACC
>site_35
AGTTAACCGATTCAGT
>site_36
ATTTTATCGATTCAGC
>site_37
CCTGAATCAATTCAGC
>site_38
GTTGAACCGATTAAGC
>site_39
GCTGAAGCGATTTCGC
>site_40
CGTTAAGCGATTCAGC
>site_41
GCTGGCGCGATTCACC
;
; Matrix parameters
;	Columns                      	16
;	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                    	Cra.1nt_upstream-noorf-ovlp-2str.16.cons1
;	AC                           	Cra.1nt_upstream-noorf-ovlp-2str.16.cons1
;	id                           	Cra.1nt_upstream-noorf-ovlp-2str.16.cons1
;	name                         	Cra.1nt_upstream-noorf-ovlp-2str.16.cons1
;	description                  	rytKaAwCGaTTCaGC
;	statistical_basis            	42 sequences
;	sites                        	42
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	9.28583
;	information.per.column       	0.580364
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	actGaAaCGaTTCaGC
;	consensus.strict.rc          	GCTGAATCGTTTCAGT
;	consensus.IUPAC              	rytKaAwCGaTTCaGC
;	consensus.IUPAC.rc           	GCTGAATCGWTTMARY
;	consensus.regexp             	[ag][ct]t[GT]aA[at]CGaTTCaGC
;	consensus.regexp.rc          	GCTGAATCG[AT]TT[AC]A[AG][CT]
;	residues.content.crude.freq  	a:0.2932|c:0.2321|g:0.1786|t:0.2961
;	G+C.content.crude.freq       	0.410714
;	residues.content.corrected.freq	a:0.2931|c:0.2316|g:0.1792|t:0.2961
;	G+C.content.corrected.freq   	0.410762
;	min(P(S|M))                  	2.11819e-31
;	max(P(S|M))                  	0.00218475
;	proba_range                  	0.00218475
;	Wmin                         	-47
;	Wmax                         	15.8
;	Wrange                       	62.8
; logo file:Cra.1nt_upstream-noorf-ovlp-2str.16.cons_quality_logo_m1.png
; logo file:Cra.1nt_upstream-noorf-ovlp-2str.16.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	0.04
;	cuser	0.52
;	csystem	0.05
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