RegulonDB
ModE matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/ModE/ModE.EcolK12_2nt_upstream.27.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 /ModE.EcolK12_2nt_upstream.27.meme_quality_logo
; Input files
; input /ModE.EcolK12_2nt_upstream.27.meme_quality_matrix.tf
; prior /ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /ModE.EcolK12_2nt_upstream.27.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 3 1 5 0 5 1 5 0 3 3 2 2 1 1 7 0 5 0 5 1 0 1 3 4 4
C 6 0 2 0 0 1 1 2 0 5 1 1 2 3 2 0 0 4 1 2 0 2 5 0 2 1 1
G 1 7 0 0 2 0 1 0 1 1 1 0 3 1 0 0 0 1 0 1 0 3 0 6 0 0 1
T 0 0 2 6 0 6 0 4 1 1 2 3 0 1 4 6 0 2 1 4 2 1 2 0 2 2 1
//
A 0.0 0.0 0.4 0.2 0.7 0.0 0.7 0.2 0.7 0.0 0.4 0.4 0.3 0.3 0.2 0.2 0.9 0.0 0.7 0.0 0.7 0.2 0.0 0.2 0.4 0.5 0.5
C 0.8 0.0 0.3 0.0 0.0 0.2 0.2 0.3 0.0 0.7 0.2 0.2 0.3 0.4 0.3 0.0 0.0 0.5 0.2 0.3 0.0 0.3 0.7 0.0 0.3 0.2 0.2
G 0.2 0.9 0.0 0.0 0.3 0.0 0.2 0.0 0.2 0.2 0.2 0.0 0.4 0.2 0.0 0.0 0.0 0.2 0.0 0.2 0.0 0.4 0.0 0.8 0.0 0.0 0.2
T 0.0 0.0 0.3 0.8 0.0 0.8 0.0 0.5 0.2 0.2 0.3 0.4 0.0 0.2 0.5 0.8 0.0 0.3 0.2 0.5 0.3 0.2 0.3 0.0 0.3 0.3 0.2
//
A -2.1 -2.1 0.3 -0.6 0.8 -2.1 0.8 -0.6 0.8 -2.1 0.3 0.3 -0.0 -0.0 -0.6 -0.6 1.1 -2.1 0.8 -2.1 0.8 -0.6 -2.1 -0.6 0.3 0.6 0.6
C 1.3 -2.1 0.3 -2.1 -2.1 -0.3 -0.3 0.3 -2.1 1.1 -0.3 -0.3 0.3 0.7 0.3 -2.1 -2.1 0.9 -0.3 0.3 -2.1 0.3 1.1 -2.1 0.3 -0.3 -0.3
G -0.3 1.5 -2.1 -2.1 0.3 -2.1 -0.3 -2.1 -0.3 -0.3 -0.3 -2.1 0.7 -0.3 -2.1 -2.1 -2.1 -0.3 -2.1 -0.3 -2.1 0.7 -2.1 1.3 -2.1 -2.1 -0.3
T -2.1 -2.1 -0.0 1.0 -2.1 1.0 -2.1 0.6 -0.6 -0.6 -0.0 0.3 -2.1 -0.6 0.6 1.0 -2.1 -0.0 -0.6 0.6 -0.0 -0.6 -0.0 -2.1 -0.0 -0.0 -0.6
//
A -0.1 -0.1 0.1 -0.1 0.5 -0.1 0.5 -0.1 0.5 -0.1 0.1 0.1 -0.0 -0.0 -0.1 -0.1 1.0 -0.1 0.5 -0.1 0.5 -0.1 -0.1 -0.1 0.1 0.3 0.3
C 1.0 -0.1 0.1 -0.1 -0.1 -0.0 -0.0 0.1 -0.1 0.7 -0.0 -0.0 0.1 0.3 0.1 -0.1 -0.1 0.5 -0.0 0.1 -0.1 0.1 0.7 -0.1 0.1 -0.0 -0.0
G -0.0 1.3 -0.1 -0.1 0.1 -0.1 -0.0 -0.1 -0.0 -0.0 -0.0 -0.1 0.3 -0.0 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0 -0.1 0.3 -0.1 1.0 -0.1 -0.1 -0.0
T -0.1 -0.1 -0.0 0.8 -0.1 0.8 -0.1 0.3 -0.1 -0.1 -0.0 0.1 -0.1 -0.1 0.3 0.8 -0.1 -0.0 -0.1 0.3 -0.0 -0.1 -0.0 -0.1 -0.0 -0.0 -0.1
//
; Sites 7
>site_0
CGCTATATACATGATTACATAGCGAAA
>site_1
CGATGTATACAAGCCTATATAGCGAAC
>site_2
CGTTATATTGTCGCCTACATAACGTTA
>site_3
CGCAACACACTTCGATACACATCACAA
>site_4
CGATATGCACGAAATAACCCTCTGCCA
>site_5
GGTTATAAATATATTTATATAGCGATT
>site_6
CGATGTCTGCCACCTTAGTGTCTGTAG
;
; Matrix parameters
; Number of sites 7
; Columns 27
; 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 CGHTATAYACWWVMYTAYAYASCGHWA
; AC CGHTATAYACWWVMYTAYAYASCGHWA
; id CGHTATAYACWWVMYTAYAYASCGHWA
; name CGHTATAYACWWVMYTAYAYASCGHWA
; description CGmtrtayaCawscytAcayasCGmaa
; statistical_basis 7 sequences
; sites 7
; nb_sites 7
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 10.9942
; information.per.column 0.407193
; max.possible.info.per.col 1.58952
; consensus.strict CGatatataCaagcttAcatagCGaaa
; consensus.strict.rc TTTCGCTATGTAAGCTTGTATATATCG
; consensus.IUPAC CGmtrtayaCawscytAcayasCGmaa
; consensus.IUPAC.rc TTKCGSTRTGTARGSWTGTRTAYAKCG
; consensus.regexp CG[ac]t[ag]ta[ct]aCa[at][cg]c[ct]tAca[ct]a[cg]CG[ac]aa
; consensus.regexp.rc TT[GT]CG[CG]T[AG]TGTA[AG]G[CG][AT]TGT[AG]TA[CT]A[GT]CG
; residues.content.crude.freq a:0.3280|c:0.2328|g:0.1587|t:0.2804
; G+C.content.crude.freq 0.391534
; residues.content.corrected.freq a:0.3234|c:0.2297|g:0.1644|t:0.2825
; G+C.content.corrected.freq 0.394072
; min(P(S|M)) 1.16947e-39
; max(P(S|M)) 5.59094e-07
; proba_range 5.59094e-07
; Wmin -50
; Wmax 22
; Wrange 72
; logo file:/ModE.EcolK12_2nt_upstream.27.meme_quality_logo_m1.png
; logo file:/ModE.EcolK12_2nt_upstream.27.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161029
; Job done 2019-06-03.161030
; Seconds 0.55
; user 0.55
; system 0.05
; cuser 0.45
; csystem 0.05