RegulonDB
RelB matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/RelB/RelB.EcolK12_1nt_upstream.15.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 /RelB.EcolK12_1nt_upstream.15.meme_quality_logo
; Input files
; input /RelB.EcolK12_1nt_upstream.15.meme_quality_matrix.tf
; prior /RelB.EcolK12_1nt_upstream.15.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /RelB.EcolK12_1nt_upstream.15.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 1 3 0 1 4 0 4 3 2 1 1 0 0
C 1 0 2 0 1 0 0 3 0 1 1 0 0 0 3
G 3 2 0 1 0 0 0 1 0 0 1 0 2 2 1
T 0 2 1 0 3 3 0 0 0 0 0 3 1 2 0
//
A 0.1 0.1 0.3 0.7 0.1 0.3 0.9 0.1 0.9 0.7 0.5 0.3 0.3 0.1 0.1
C 0.2 0.0 0.4 0.0 0.2 0.0 0.0 0.6 0.0 0.2 0.2 0.0 0.0 0.0 0.6
G 0.6 0.4 0.0 0.2 0.0 0.0 0.0 0.2 0.0 0.0 0.2 0.0 0.4 0.4 0.2
T 0.1 0.5 0.3 0.1 0.7 0.7 0.1 0.1 0.1 0.1 0.1 0.7 0.3 0.5 0.1
//
A -1.6 -1.6 -0.1 0.8 -1.6 -0.1 1.1 -1.6 1.1 0.8 0.5 -0.1 -0.1 -1.6 -1.6
C 0.2 -1.6 0.8 -1.6 0.2 -1.6 -1.6 1.1 -1.6 0.2 0.2 -1.6 -1.6 -1.6 1.1
G 1.1 0.8 -1.6 0.2 -1.6 -1.6 -1.6 0.2 -1.6 -1.6 0.2 -1.6 0.8 0.8 0.2
T -1.6 0.4 -0.1 -1.6 0.8 0.8 -1.6 -1.6 -1.6 -1.6 -1.6 0.8 -0.1 0.4 -1.6
//
A -0.1 -0.1 -0.0 0.5 -0.1 -0.0 0.9 -0.1 0.9 0.5 0.2 -0.0 -0.0 -0.1 -0.1
C 0.0 -0.1 0.3 -0.1 0.0 -0.1 -0.1 0.7 -0.1 0.0 0.0 -0.1 -0.1 -0.1 0.7
G 0.7 0.3 -0.1 0.0 -0.1 -0.1 -0.1 0.0 -0.1 -0.1 0.0 -0.1 0.3 0.3 0.0
T -0.1 0.2 -0.0 -0.1 0.5 0.5 -0.1 -0.1 -0.1 -0.1 -0.1 0.5 -0.0 0.2 -0.1
//
; Sites 4
>site_0
GTAATTACAAATGTC
>site_1
GTCATTACAAGTATC
>site_2
CGCACTACAACATGC
>site_3
GGTGTAAGACATGGG
;
; Matrix parameters
; Number of sites 4
; Columns 15
; 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 GKHATTACAAVTDKC
; AC GKHATTACAAVTDKC
; id GKHATTACAAVTDKC
; name GKHATTACAAVTDKC
; description SkcrytASAmvtgkS
; statistical_basis 4 sequences
; sites 4
; nb_sites 4
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 6.43658
; information.per.column 0.429105
; max.possible.info.per.col 1.58873
; consensus.strict GgcattACAaatggC
; consensus.strict.rc GCCATTTGTAATGCC
; consensus.IUPAC SkcrytASAmvtgkS
; consensus.IUPAC.rc SMCABKTSTARYGMS
; consensus.regexp [CG][gt]c[ag][ct]tA[CG]A[ac][acg]tg[gt][CG]
; consensus.regexp.rc [CG][AC]CA[CGT][GT]T[CG]TA[AG][CT]G[AC][CG]
; residues.content.crude.freq a:0.3333|c:0.2000|g:0.2167|t:0.2500
; G+C.content.crude.freq 0.416667
; residues.content.corrected.freq a:0.3249|c:0.2015|g:0.2142|t:0.2595
; G+C.content.corrected.freq 0.415682
; min(P(S|M)) 6.58855e-21
; max(P(S|M)) 0.000454318
; proba_range 0.000454318
; Wmin -24.2
; Wmax 13.2
; Wrange 37.4
; logo file:/RelB.EcolK12_1nt_upstream.15.meme_quality_logo_m1.png
; logo file:/RelB.EcolK12_1nt_upstream.15.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161059
; Seconds 0.54
; user 0.54
; system 0.05
; cuser 0.38
; csystem 0.04