RegulonDB

PutA matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/PutA/PutA.EcolK12_1nt_upstream.6.meme

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 /PutA.EcolK12_1nt_upstream.6.meme_quality_logo
; Input files
;	input	/PutA.EcolK12_1nt_upstream.6.meme_quality_matrix.tf
;	prior	/PutA.EcolK12_1nt_upstream.6.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/PutA.EcolK12_1nt_upstream.6.meme_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	0.29093
;		c	0.20756
;		g	0.20418
;		t	0.29732
A	0	0	0	5	5	0
C	0	0	5	0	0	5
G	0	5	0	0	0	0
T	5	0	0	0	0	0
//
A  0.0  0.0  0.0  0.9  0.9  0.0
C  0.0  0.0  0.9  0.0  0.0  0.9
G  0.0  0.9  0.0  0.0  0.0  0.0
T  0.9  0.0  0.0  0.0  0.0  0.0
//
A -1.8 -1.8 -1.8  1.1  1.1 -1.8
C -1.8 -1.8  1.4 -1.8 -1.8  1.4
G -1.8  1.4 -1.8 -1.8 -1.8 -1.8
T  1.1 -1.8 -1.8 -1.8 -1.8 -1.8
//
A -0.1 -0.1 -0.1  1.0  1.0 -0.1
C -0.1 -0.1  1.2 -0.1 -0.1  1.2
G -0.1  1.3 -0.1 -0.1 -0.1 -0.1
T  1.0 -0.1 -0.1 -0.1 -0.1 -0.1
//
; Sites	5
>site_0
TGCAAC
>site_1
TGCAAC
>site_2
TGCAAC
>site_3
TGCAAC
>site_4
TGCAAC
;
; Matrix parameters
;	Number of sites              	5
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	A|C|G|T
;	Prior                        	A:0.290929484294843|C:0.207560750607506|G:0.204184816848168|T:0.297324948249482|a:0.290929484294843|c:0.207560750607506|g:0.204184816848168|t:0.297324948249482
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	TGCAAC
;	AC                           	TGCAAC
;	id                           	TGCAAC
;	name                         	TGCAAC
;	description                  	TGCAAC
;	statistical_basis            	5 sequences
;	sites                        	5
;	nb_sites                     	5
;	min.prior                    	0.204185
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.3104
;	information.per.column       	0.885067
;	max.possible.info.per.col    	1.58873
;	consensus.strict             	TGCAAC
;	consensus.strict.rc          	GTTGCA
;	consensus.IUPAC              	TGCAAC
;	consensus.IUPAC.rc           	GTTGCA
;	consensus.regexp             	TGCAAC
;	consensus.regexp.rc          	GTTGCA
;	residues.content.crude.freq  	a:0.3333|c:0.3333|g:0.1667|t:0.1667
;	G+C.content.crude.freq       	0.5
;	residues.content.corrected.freq	a:0.3263|c:0.3124|g:0.1729|t:0.1884
;	G+C.content.corrected.freq   	0.485291
;	min(P(S|M))                  	1.5789e-09
;	max(P(S|M))                  	0.448574
;	proba_range                  	0.448574
;	Wmin                         	-10.8
;	Wmax                         	7.7
;	Wrange                       	18.5
; logo file:/PutA.EcolK12_1nt_upstream.6.meme_quality_logo_m1.png
; logo file:/PutA.EcolK12_1nt_upstream.6.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.161059
; Job done	2019-06-03.161100
; Seconds	0.54
;	user	0.54
;	system	0.05
;	cuser	0.37
;	csystem	0.04
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