RegulonDB
NrdR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/NrdR/NrdR.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 /NrdR.EcolK12_2nt_upstream.19.meme_quality_logo
; Input files
; input /NrdR.EcolK12_2nt_upstream.19.meme_quality_matrix.tf
; prior /NrdR.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 /NrdR.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 4 3 3 0 2 0 2 6 0 6 0 5 0 3 0 0 0 1
C 0 1 1 2 1 1 6 0 0 1 0 0 0 0 0 0 0 0 1
G 1 0 1 0 1 2 0 0 0 2 0 0 1 1 0 6 1 5 1
T 5 1 1 1 4 1 0 4 0 3 0 6 0 5 3 0 5 1 3
//
A 0.0 0.6 0.5 0.5 0.0 0.3 0.0 0.3 0.9 0.0 0.9 0.0 0.8 0.0 0.5 0.0 0.0 0.0 0.2
C 0.0 0.2 0.2 0.3 0.2 0.2 0.9 0.0 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2
G 0.2 0.0 0.2 0.0 0.2 0.3 0.0 0.0 0.0 0.3 0.0 0.0 0.2 0.2 0.0 0.9 0.2 0.7 0.2
T 0.8 0.2 0.2 0.2 0.6 0.2 0.0 0.6 0.0 0.5 0.0 0.9 0.0 0.8 0.5 0.0 0.8 0.2 0.5
//
A -1.9 0.7 0.5 0.5 -1.9 0.1 -1.9 0.1 1.1 -1.9 1.1 -1.9 1.0 -1.9 0.5 -1.9 -1.9 -1.9 -0.5
C -1.9 -0.2 -0.2 0.4 -0.2 -0.2 1.5 -1.9 -1.9 -0.2 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 -0.2
G -0.2 -1.9 -0.2 -1.9 -0.2 0.4 -1.9 -1.9 -1.9 0.4 -1.9 -1.9 -0.2 -0.2 -1.9 1.5 -0.2 1.3 -0.2
T 0.9 -0.5 -0.5 -0.5 0.7 -0.5 -1.9 0.7 -1.9 0.5 -1.9 1.1 -1.9 0.9 0.5 -1.9 0.9 -0.5 0.5
//
A -0.1 0.5 0.2 0.2 -0.1 0.0 -0.1 0.0 1.0 -0.1 1.0 -0.1 0.7 -0.1 0.2 -0.1 -0.1 -0.1 -0.1
C -0.1 -0.0 -0.0 0.1 -0.0 -0.0 1.3 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0
G -0.0 -0.1 -0.0 -0.1 -0.0 0.1 -0.1 -0.1 -0.1 0.1 -0.1 -0.1 -0.0 -0.0 -0.1 1.3 -0.0 1.0 -0.0
T 0.7 -0.1 -0.1 -0.1 0.4 -0.1 -0.1 0.4 -0.1 0.2 -0.1 1.0 -0.1 0.7 0.2 -0.1 0.7 -0.1 0.2
//
; Sites 6
>site_0
TATTTGCTATATATTGTGT
>site_1
TACCCCCTATATATAGTGT
>site_2
TAAAGTCTATATATAGTGC
>site_3
TCACTGCAAGATAGTGTGA
>site_4
TTAATACAACATATTGGGT
>site_5
GAGATACTAGATGTAGTTG
;
; Matrix parameters
; Number of sites 6
; 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 TAAMTNCWAKATATWGTGT
; AC TAAMTNCWAKATATWGTGT
; id TAAMTNCWAKATATWGTGT
; name TAAMTNCWAKATATWGTGT
; description taamtrCwAkATatwGtGt
; statistical_basis 6 sequences
; sites 6
; nb_sites 6
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 9.42372
; information.per.column 0.495985
; max.possible.info.per.col 1.58952
; consensus.strict taaatgCtAtATataGtGt
; consensus.strict.rc ACACTATATATAGCATTTA
; consensus.IUPAC taamtrCwAkATatwGtGt
; consensus.IUPAC.rc ACACWATATMTWGYAKTTA
; consensus.regexp taa[ac]t[ag]C[at]A[gt]ATat[at]GtGt
; consensus.regexp.rc ACAC[AT]ATAT[AC]T[AT]G[CT]A[GT]TTA
; residues.content.crude.freq a:0.3070|c:0.1228|g:0.1930|t:0.3772
; G+C.content.crude.freq 0.315789
; residues.content.corrected.freq a:0.3047|c:0.1350|g:0.1946|t:0.3657
; G+C.content.corrected.freq 0.32951
; min(P(S|M)) 3.14834e-27
; max(P(S|M)) 0.000242855
; proba_range 0.000242855
; Wmin -32.6
; Wmax 16.4
; Wrange 49
; logo file:/NrdR.EcolK12_2nt_upstream.19.meme_quality_logo_m1.png
; logo file:/NrdR.EcolK12_2nt_upstream.19.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161045
; Job done 2019-06-03.161046
; Seconds 0.56
; user 0.56
; system 0.06
; cuser 0.41
; csystem 0.05