RegulonDB
DeoR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/DeoR/DeoR.EcolK12_2nt_upstream.19.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 /DeoR.EcolK12_2nt_upstream.19.meme_quality_logo
; Input files
; input /DeoR.EcolK12_2nt_upstream.19.meme_quality_matrix.tf
; prior /DeoR.EcolK12_2nt_upstream.19.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /DeoR.EcolK12_2nt_upstream.19.meme_quality_matrix_info.txt
; Output format tab
; pseudo-weight 1
; Background model
; Strand undef
; Background pseudo-frequency 0.01
; Residue probabilities
; a 0.29114
; c 0.20781
; g 0.20402
; t 0.29702
A 0 0 0 0 0 0 5 2 4 5 2 0 1 2 5 3 1 6 0
C 0 1 0 1 0 0 0 2 0 2 0 0 3 1 0 0 5 0 0
G 1 2 0 6 0 4 2 3 0 0 0 4 2 0 1 3 1 0 1
T 6 4 7 0 7 3 0 0 3 0 5 3 1 4 1 1 0 1 6
//
A 0.0 0.0 0.0 0.0 0.0 0.0 0.7 0.3 0.5 0.7 0.3 0.0 0.2 0.3 0.7 0.4 0.2 0.8 0.0
C 0.0 0.2 0.0 0.2 0.0 0.0 0.0 0.3 0.0 0.3 0.0 0.0 0.4 0.2 0.0 0.0 0.7 0.0 0.0
G 0.2 0.3 0.0 0.8 0.0 0.5 0.3 0.4 0.0 0.0 0.0 0.5 0.3 0.0 0.2 0.4 0.2 0.0 0.2
T 0.8 0.5 0.9 0.0 0.9 0.4 0.0 0.0 0.4 0.0 0.7 0.4 0.2 0.5 0.2 0.2 0.0 0.2 0.8
//
A -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 0.8 -0.0 0.6 0.8 -0.0 -2.1 -0.6 -0.0 0.8 0.3 -0.6 1.0 -2.1
C -2.1 -0.3 -2.1 -0.3 -2.1 -2.1 -2.1 0.3 -2.1 0.3 -2.1 -2.1 0.7 -0.3 -2.1 -2.1 1.1 -2.1 -2.1
G -0.3 0.3 -2.1 1.3 -2.1 0.9 0.3 0.7 -2.1 -2.1 -2.1 0.9 0.3 -2.1 -0.3 0.7 -0.3 -2.1 -0.3
T 1.0 0.6 1.1 -2.1 1.1 0.3 -2.1 -2.1 0.3 -2.1 0.8 0.3 -0.6 0.6 -0.6 -0.6 -2.1 -0.6 1.0
//
A -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.5 -0.0 0.3 0.5 -0.0 -0.1 -0.1 -0.0 0.5 0.1 -0.1 0.8 -0.1
C -0.1 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 0.1 -0.1 0.1 -0.1 -0.1 0.3 -0.0 -0.1 -0.1 0.7 -0.1 -0.1
G -0.0 0.1 -0.1 1.0 -0.1 0.5 0.1 0.3 -0.1 -0.1 -0.1 0.5 0.1 -0.1 -0.0 0.3 -0.0 -0.1 -0.0
T 0.8 0.3 1.0 -0.1 1.0 0.1 -0.1 -0.1 0.1 -0.1 0.5 0.1 -0.1 0.3 -0.1 -0.1 -0.1 -0.1 0.8
//
; Sites 7
>site_0
TTTGTTAGTATTCTAACAT
>site_1
TGTGTTAGAATTCTAACAT
>site_2
TTTGTTACTCTGCTTACAT
>site_3
TTTGTGAAAATTTTATCAT
>site_4
TTTCTGGCACTGGAAGCAG
>site_5
TGTGTGAAAAAGAAGGGAT
>site_6
GCTGTGGGTAAGGCAGATT
;
; Matrix parameters
; Number of sites 7
; Columns 19
; Rows 4
; Alphabet A|C|G|T
; Prior A:0.291144263562772|C:0.207810681831126|G:0.204024081631615|T:0.297020972974487|a:0.291144263562772|c:0.207810681831126|g:0.204024081631615|t:0.297020972974487
; program transfac
; matrix.nb 1
; accession TKTGTKAVWATKSWARCAT
; AC TKTGTKAVWATKSWARCAT
; id TKTGTKAVWATKSWARCAT
; name TKTGTKAVWATKSWARCAT
; description tkTGTkrswmtkstarCat
; statistical_basis 7 sequences
; sites 7
; nb_sites 7
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 9.07857
; information.per.column 0.47782
; max.possible.info.per.col 1.58952
; consensus.strict ttTGTgagaatgctagCat
; consensus.strict.rc ATGCTAGCATTCTCACAAA
; consensus.IUPAC tkTGTkrswmtkstarCat
; consensus.IUPAC.rc ATGYTASMAKWSYMACAMA
; consensus.regexp t[gt]TGT[gt][ag][cg][at][ac]t[gt][cg]ta[ag]Cat
; consensus.regexp.rc ATG[CT]TA[CG][AC]A[GT][AT][CG][CT][AC]ACA[AC]A
; residues.content.crude.freq a:0.2707|c:0.1128|g:0.2256|t:0.3910
; G+C.content.crude.freq 0.338346
; residues.content.corrected.freq a:0.2732|c:0.1247|g:0.2229|t:0.3792
; G+C.content.corrected.freq 0.347532
; min(P(S|M)) 1.65006e-29
; max(P(S|M)) 0.000110683
; proba_range 0.000110683
; Wmin -38.1
; Wmax 16.7
; Wrange 54.8
; logo file:/DeoR.EcolK12_2nt_upstream.19.meme_quality_logo_m1.png
; logo file:/DeoR.EcolK12_2nt_upstream.19.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.6
; user 0.6
; system 0.07
; cuser 0.42
; csystem 0.05