RegulonDB

AscG matrix and aligment

matrix-quality result

Command: 
AscG.1nt_upstream-noorf-ovlp-2str.12.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 AscG.1nt_upstream-noorf-ovlp-2str.12.cons_quality_logo
; Input files
;	input	AscG.1nt_upstream-noorf-ovlp-2str.12.cons_quality_matrix.tf
;	prior	AscG.1nt_upstream-noorf-ovlp-2str.12.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	AscG.1nt_upstream-noorf-ovlp-2str.12.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	2	0	0	8	9	9	0	4	3	0	3	2
C	1	0	0	1	0	0	8	3	1	1	0	3
G	5	0	9	0	0	0	0	2	3	5	2	0
T	1	9	0	0	0	0	1	0	2	3	4	4
//
a  0.2  0.0  0.0  0.8  0.9  0.9  0.0  0.4  0.3  0.0  0.3  0.2
c  0.1  0.0  0.0  0.1  0.0  0.0  0.8  0.3  0.1  0.1  0.0  0.3
g  0.5  0.0  0.9  0.0  0.0  0.0  0.0  0.2  0.3  0.5  0.2  0.0
t  0.1  0.9  0.0  0.0  0.0  0.0  0.1  0.0  0.2  0.3  0.4  0.4
//
a -0.2 -2.3 -2.3  1.0  1.2  1.2 -2.3  0.4  0.1 -2.3  0.1 -0.2
c -0.5 -2.3 -2.3 -0.5 -2.3 -2.3  1.4  0.4 -0.5 -0.5 -2.3  0.4
g  0.9 -2.3  1.5 -2.3 -2.3 -2.3 -2.3  0.1  0.4  0.9  0.1 -2.3
t -0.8  1.1 -2.3 -2.3 -2.3 -2.3 -0.8 -2.3 -0.3  0.1  0.4  0.4
//
a -0.1 -0.1 -0.1  0.9  1.1  1.1 -0.1  0.2  0.0 -0.1  0.0 -0.1
c -0.1 -0.0 -0.0 -0.1 -0.0 -0.0  1.1  0.1 -0.1 -0.1 -0.0  0.1
g  0.5 -0.0  1.4 -0.0 -0.0 -0.0 -0.0  0.0  0.1  0.5  0.0 -0.0
t -0.1  1.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  0.0  0.2  0.2
//
; Sites	9
>site_0
ATGAAACAAGAC
>site_1
TTGCAACAATTA
>site_2
ATGAAACGCGGT
>site_3
GTGAAACATTGC
>site_4
CTGAAACGTTAA
>site_5
GTGAAACAGCTT
>site_6
GTGAAATCAGAT
>site_7
GTGAAACCGGTC
>site_8
GTGAAACCGGTT
;
; Matrix parameters
;	Columns                      	12
;	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                    	AscG.1nt_upstream-noorf-ovlp-2str.12.cons1
;	AC                           	AscG.1nt_upstream-noorf-ovlp-2str.12.cons1
;	id                           	AscG.1nt_upstream-noorf-ovlp-2str.12.cons1
;	name                         	AscG.1nt_upstream-noorf-ovlp-2str.12.cons1
;	description                  	gTGAAACvrkdy
;	statistical_basis            	9 sequences
;	sites                        	9
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.8511
;	information.per.column       	0.570925
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	gTGAAACcggtc
;	consensus.strict.rc          	GACCGGTTTCAC
;	consensus.IUPAC              	gTGAAACvrkdy
;	consensus.IUPAC.rc           	RHMYBGTTTCAC
;	consensus.regexp             	gTGAAAC[acg][ag][gt][agt][ct]
;	consensus.regexp.rc          	[AG][ACT][AC][CT][CGT]GTTTCAC
;	residues.content.crude.freq  	a:0.3704|c:0.1667|g:0.2407|t:0.2222
;	G+C.content.crude.freq       	0.407407
;	residues.content.corrected.freq	a:0.3624|c:0.1708|g:0.2372|t:0.2297
;	G+C.content.corrected.freq   	0.407942
;	min(P(S|M))                  	4.02201e-19
;	max(P(S|M))                  	0.00354922
;	proba_range                  	0.00354922
;	Wmin                         	-24.4
;	Wmax                         	11
;	Wrange                       	35.4
; logo file:AscG.1nt_upstream-noorf-ovlp-2str.12.cons_quality_logo_m1.png
; logo file:AscG.1nt_upstream-noorf-ovlp-2str.12.cons_quality_logo_m1_rc.png
; Host name	compute-1-7.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.31
;	system	0.04
;	cuser	0.48
;	csystem	0.06
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