RegulonDB
RutR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/RutR/RutR.EcolK12_1nt_upstream.20.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 /RutR.EcolK12_1nt_upstream.20.meme_quality_logo
; Input files
; input /RutR.EcolK12_1nt_upstream.20.meme_quality_matrix.tf
; prior /RutR.EcolK12_1nt_upstream.20.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /RutR.EcolK12_1nt_upstream.20.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 1 1 1 4 0 1 3 2 0 0 2 0 1 0 2 5 1 0 1 0
C 1 1 0 1 5 4 0 0 1 0 1 0 0 5 2 0 4 0 1 1
G 0 0 4 0 0 0 2 1 1 0 2 5 0 0 0 0 0 2 0 1
T 3 3 0 0 0 0 0 2 3 5 0 0 4 0 1 0 0 3 3 3
//
A 0.2 0.2 0.2 0.7 0.0 0.2 0.5 0.4 0.0 0.0 0.4 0.0 0.2 0.0 0.4 0.9 0.2 0.0 0.2 0.0
C 0.2 0.2 0.0 0.2 0.9 0.7 0.0 0.0 0.2 0.0 0.2 0.0 0.0 0.9 0.4 0.0 0.7 0.0 0.2 0.2
G 0.0 0.0 0.7 0.0 0.0 0.0 0.4 0.2 0.2 0.0 0.4 0.9 0.0 0.0 0.0 0.0 0.0 0.4 0.0 0.2
T 0.5 0.5 0.0 0.0 0.0 0.0 0.0 0.4 0.5 0.9 0.0 0.0 0.7 0.0 0.2 0.0 0.0 0.5 0.5 0.5
//
A -0.3 -0.3 -0.3 0.9 -1.8 -0.3 0.6 0.3 -1.8 -1.8 0.3 -1.8 -0.3 -1.8 0.3 1.1 -0.3 -1.8 -0.3 -1.8
C -0.0 -0.0 -1.8 -0.0 1.4 1.2 -1.8 -1.8 -0.0 -1.8 -0.0 -1.8 -1.8 1.4 0.6 -1.8 1.2 -1.8 -0.0 -0.0
G -1.8 -1.8 1.2 -1.8 -1.8 -1.8 0.6 -0.0 -0.0 -1.8 0.6 1.4 -1.8 -1.8 -1.8 -1.8 -1.8 0.6 -1.8 -0.0
T 0.6 0.6 -1.8 -1.8 -1.8 -1.8 -1.8 0.3 0.6 1.1 -1.8 -1.8 0.9 -1.8 -0.3 -1.8 -1.8 0.6 0.6 0.6
//
A -0.1 -0.1 -0.1 0.6 -0.1 -0.1 0.3 0.1 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 0.1 1.0 -0.1 -0.1 -0.1 -0.1
C -0.0 -0.0 -0.1 -0.0 1.2 0.9 -0.1 -0.1 -0.0 -0.1 -0.0 -0.1 -0.1 1.2 0.2 -0.1 0.9 -0.1 -0.0 -0.0
G -0.1 -0.1 0.9 -0.1 -0.1 -0.1 0.2 -0.0 -0.0 -0.1 0.2 1.3 -0.1 -0.1 -0.1 -0.1 -0.1 0.2 -0.1 -0.0
T 0.3 0.3 -0.1 -0.1 -0.1 -0.1 -0.1 0.1 0.3 1.0 -0.1 -0.1 0.6 -0.1 -0.1 -0.1 -0.1 0.3 0.3 0.3
//
; Sites 5
>site_0
TTGACCATTTGGTCCACTTT
>site_1
TTGACCGTTTAGTCCACTTT
>site_2
TAGACCGACTGGTCTACTAC
>site_3
CCACCCAGGTAGTCAACGTT
>site_4
ATGACAAATTCGACAAAGCG
;
; Matrix parameters
; Number of sites 5
; Columns 20
; 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 TTGACCRDTTVGTCHACKTT
; AC TTGACCRDTTVGTCHACKTT
; id TTGACCRDTTVGTCHACKTT
; name TTGACCRDTTVGTCHACKTT
; description ttGaCCrwtTrGtCmACktt
; statistical_basis 5 sequences
; sites 5
; nb_sites 5
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 9.85995
; information.per.column 0.492998
; max.possible.info.per.col 1.58873
; consensus.strict ttGaCCaatTgGtCcACttt
; consensus.strict.rc AAAGTGGACCAATTGGTCAA
; consensus.IUPAC ttGaCCrwtTrGtCmACktt
; consensus.IUPAC.rc AAMGTKGACYAAWYGGTCAA
; consensus.regexp ttGaCC[ag][at]tT[ag]GtC[ac]AC[gt]tt
; consensus.regexp.rc AA[AC]GT[GT]GAC[CT]AA[AT][CT]GGTCAA
; residues.content.crude.freq a:0.2500|c:0.2700|g:0.1800|t:0.3000
; G+C.content.crude.freq 0.45
; residues.content.corrected.freq a:0.2568|c:0.2596|g:0.1840|t:0.2996
; G+C.content.corrected.freq 0.443624
; min(P(S|M)) 1.39248e-29
; max(P(S|M)) 7.57203e-05
; proba_range 7.57203e-05
; Wmin -35.9
; Wmax 17.8
; Wrange 53.7
; logo file:/RutR.EcolK12_1nt_upstream.20.meme_quality_logo_m1.png
; logo file:/RutR.EcolK12_1nt_upstream.20.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161114
; Job done 2019-06-03.161115
; Seconds 0.55
; user 0.55
; system 0.05
; cuser 0.42
; csystem 0.05