RegulonDB
DcuR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/DcuR/DcuR.EcolK12_1nt_upstream.21.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 /DcuR.EcolK12_1nt_upstream.21.meme_quality_logo
; Input files
; input /DcuR.EcolK12_1nt_upstream.21.meme_quality_matrix.tf
; prior /DcuR.EcolK12_1nt_upstream.21.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /DcuR.EcolK12_1nt_upstream.21.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 3 4 0 0 3 3 0 0 2 6 5 0 0 2 1 1 3 3 6 3
C 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 2 0 0 0 0 2
G 1 2 2 0 2 1 0 0 0 0 0 0 2 1 0 0 1 1 0 0 1
T 4 0 0 5 4 2 3 6 6 4 0 0 4 5 4 3 4 2 3 0 0
//
A 0.0 0.5 0.6 0.0 0.0 0.5 0.5 0.0 0.0 0.3 0.9 0.8 0.0 0.0 0.3 0.2 0.2 0.5 0.5 0.9 0.5
C 0.2 0.2 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.3 0.0 0.0 0.0 0.0 0.3
G 0.2 0.3 0.3 0.0 0.3 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.2 0.0 0.0 0.2 0.2 0.0 0.0 0.2
T 0.6 0.0 0.0 0.8 0.6 0.3 0.5 0.9 0.9 0.6 0.0 0.0 0.6 0.8 0.6 0.5 0.6 0.3 0.5 0.0 0.0
//
A -1.9 0.5 0.7 -1.9 -1.9 0.5 0.5 -1.9 -1.9 0.1 1.1 1.0 -1.9 -1.9 0.1 -0.5 -0.5 0.5 0.5 1.1 0.5
C -0.2 -0.2 -1.9 -0.2 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 -0.2 -1.9 -1.9 -1.9 0.4 -1.9 -1.9 -1.9 -1.9 0.4
G -0.2 0.4 0.4 -1.9 0.4 -0.2 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 0.4 -0.2 -1.9 -1.9 -0.2 -0.2 -1.9 -1.9 -0.2
T 0.7 -1.9 -1.9 0.9 0.7 0.1 0.5 1.1 1.1 0.7 -1.9 -1.9 0.7 0.9 0.7 0.5 0.7 0.1 0.5 -1.9 -1.9
//
A -0.1 0.2 0.5 -0.1 -0.1 0.2 0.2 -0.1 -0.1 0.0 1.0 0.7 -0.1 -0.1 0.0 -0.1 -0.1 0.2 0.2 1.0 0.2
C -0.0 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 -0.1 0.1
G -0.0 0.1 0.1 -0.1 0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.1 -0.0 -0.1 -0.1 -0.0 -0.0 -0.1 -0.1 -0.0
T 0.4 -0.1 -0.1 0.7 0.4 0.0 0.2 1.0 1.0 0.4 -0.1 -0.1 0.4 0.7 0.4 0.2 0.4 0.0 0.2 -0.1 -0.1
//
; Sites 6
>site_0
TGATTAATTTAATTACTAAAC
>site_1
TAATGATTTTAAGTTTTTTAA
>site_2
TAATTGATTTAATGAATAAAA
>site_3
CGGTGTTTTTAATTTCAAAAC
>site_4
TAGTTAATTAACTTTTGTTAG
>site_5
GCACTTTTTAAAGTTTTGTAA
;
; Matrix parameters
; Number of sites 6
; Columns 21
; 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 TRRTKWWTTWAAKTWYTWWAM
; AC TRRTKWWTTWAAKTWYTWWAM
; id TRRTKWWTTWAAKTWYTWWAM
; name TRRTKWWTTWAAKTWYTWWAM
; description trrtkwwTTwAaktwytwwAm
; statistical_basis 6 sequences
; sites 6
; nb_sites 6
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 9.21303
; information.per.column 0.438716
; max.possible.info.per.col 1.58873
; consensus.strict taattaaTTtAatttttaaAa
; consensus.strict.rc TTTTAAAAATTAAATTAATTA
; consensus.IUPAC trrtkwwTTwAaktwytwwAm
; consensus.IUPAC.rc KTWWARWAMTTWAAWWMAYYA
; consensus.regexp t[ag][ag]t[gt][at][at]TT[at]Aa[gt]t[at][ct]t[at][at]A[ac]
; consensus.regexp.rc [GT]T[AT][AT]A[AG][AT]A[AC]TT[AT]AA[AT][AT][AC]A[CT][CT]A
; residues.content.crude.freq a:0.3571|c:0.0635|g:0.1111|t:0.4683
; G+C.content.crude.freq 0.174603
; residues.content.corrected.freq a:0.3477|c:0.0841|g:0.1244|t:0.4438
; G+C.content.corrected.freq 0.208481
; min(P(S|M)) 1.96547e-32
; max(P(S|M)) 4.74055e-05
; proba_range 4.74055e-05
; Wmin -40.9
; Wmax 15.8
; Wrange 56.7
; logo file:/DcuR.EcolK12_1nt_upstream.21.meme_quality_logo_m1.png
; logo file:/DcuR.EcolK12_1nt_upstream.21.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.6
; user 0.6
; system 0.06
; cuser 0.46
; csystem 0.05