RegulonDB
MntR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/MntR/MntR.EcolK12_2nt_upstream.25.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 /MntR.EcolK12_2nt_upstream.25.meme_quality_logo
; Input files
; input /MntR.EcolK12_2nt_upstream.25.meme_quality_matrix.tf
; prior /MntR.EcolK12_2nt_upstream.25.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /MntR.EcolK12_2nt_upstream.25.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 4 4 0 4 0 6 0 0 4 3 4 3 0 0 0 6 0 2 0 1 2 1 4 0 3
C 0 0 1 0 0 0 0 6 2 2 1 0 0 6 0 0 0 0 0 1 0 0 1 1 0
G 2 1 0 0 0 0 6 0 0 0 0 3 6 0 0 0 0 4 0 1 0 1 1 1 2
T 0 1 5 2 6 0 0 0 0 1 1 0 0 0 6 0 6 0 6 3 4 4 0 4 1
//
A 0.6 0.6 0.0 0.6 0.0 0.9 0.0 0.0 0.6 0.5 0.6 0.5 0.0 0.0 0.0 0.9 0.0 0.3 0.0 0.2 0.3 0.2 0.6 0.0 0.5
C 0.0 0.0 0.2 0.0 0.0 0.0 0.0 0.9 0.3 0.3 0.2 0.0 0.0 0.9 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.2 0.2 0.0
G 0.3 0.2 0.0 0.0 0.0 0.0 0.9 0.0 0.0 0.0 0.0 0.5 0.9 0.0 0.0 0.0 0.0 0.6 0.0 0.2 0.0 0.2 0.2 0.2 0.3
T 0.0 0.2 0.8 0.3 0.9 0.0 0.0 0.0 0.0 0.2 0.2 0.0 0.0 0.0 0.9 0.0 0.9 0.0 0.9 0.5 0.6 0.6 0.0 0.6 0.2
//
A 0.7 0.7 -1.9 0.7 -1.9 1.1 -1.9 -1.9 0.7 0.5 0.7 0.5 -1.9 -1.9 -1.9 1.1 -1.9 0.1 -1.9 -0.5 0.1 -0.5 0.7 -1.9 0.5
C -1.9 -1.9 -0.2 -1.9 -1.9 -1.9 -1.9 1.5 0.4 0.4 -0.2 -1.9 -1.9 1.5 -1.9 -1.9 -1.9 -1.9 -1.9 -0.2 -1.9 -1.9 -0.2 -0.2 -1.9
G 0.4 -0.2 -1.9 -1.9 -1.9 -1.9 1.5 -1.9 -1.9 -1.9 -1.9 0.8 1.5 -1.9 -1.9 -1.9 -1.9 1.1 -1.9 -0.2 -1.9 -0.2 -0.2 -0.2 0.4
T -1.9 -0.5 0.9 0.1 1.1 -1.9 -1.9 -1.9 -1.9 -0.5 -0.5 -1.9 -1.9 -1.9 1.1 -1.9 1.1 -1.9 1.1 0.5 0.7 0.7 -1.9 0.7 -0.5
//
A 0.5 0.5 -0.1 0.5 -0.1 1.0 -0.1 -0.1 0.5 0.2 0.5 0.2 -0.1 -0.1 -0.1 1.0 -0.1 0.0 -0.1 -0.1 0.0 -0.1 0.5 -0.1 0.2
C -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 1.3 0.1 0.1 -0.0 -0.1 -0.1 1.3 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.0 -0.0 -0.1
G 0.1 -0.0 -0.1 -0.1 -0.1 -0.1 1.3 -0.1 -0.1 -0.1 -0.1 0.4 1.3 -0.1 -0.1 -0.1 -0.1 0.6 -0.1 -0.0 -0.1 -0.0 -0.0 -0.0 0.1
T -0.1 -0.1 0.7 0.0 1.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 1.0 -0.1 1.0 -0.1 1.0 0.2 0.4 0.4 -0.1 0.4 -0.1
//
; Sites 6
>site_0
GATATAGCACAGGCTATATTATATA
>site_1
AACATAGCAAAGGCTATGTTTTAGA
>site_2
AATTTAGCCAAAGCTATGTTTAGTG
>site_3
AATATAGCCTAAGCTATGTCTGATT
>site_4
AGTATAGCACCGGCTATGTGTTCCG
>site_5
GTTTTAGCAATAGCTATATAATATA
;
; Matrix parameters
; Number of sites 6
; Columns 25
; 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 RATWTAGCMMARGCTATRTTWTATR
; AC RATWTAGCMMARGCTATRTTWTATR
; id RATWTAGCMMARGCTATRTTWTATR
; name RATWTAGCMMARGCTATRTTWTATR
; description ratwTAGCmmarGCTATRTtwtatr
; statistical_basis 6 sequences
; sites 6
; nb_sites 6
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 14.2697
; information.per.column 0.570788
; max.possible.info.per.col 1.58952
; consensus.strict aataTAGCaaagGCTATGTtttata
; consensus.strict.rc TATAAAACATAGCCTTTGCTATATT
; consensus.IUPAC ratwTAGCmmarGCTATRTtwtatr
; consensus.IUPAC.rc YATAWAAYATAGCYTKKGCTAWATY
; consensus.regexp [ag]at[at]TAGC[ac][ac]a[ag]GCTAT[AG]Tt[at]tat[ag]
; consensus.regexp.rc [CT]ATA[AT]AA[CT]ATAGC[CT]T[GT][GT]GCTA[AT]AT[CT]
; residues.content.crude.freq a:0.3400|c:0.1400|g:0.1867|t:0.3333
; G+C.content.crude.freq 0.326667
; residues.content.corrected.freq a:0.3330|c:0.1497|g:0.1891|t:0.3281
; G+C.content.corrected.freq 0.338834
; min(P(S|M)) 5.8474e-38
; max(P(S|M)) 8.92428e-05
; proba_range 8.92428e-05
; Wmin -47.2
; Wmax 23.5
; Wrange 70.7
; logo file:/MntR.EcolK12_2nt_upstream.25.meme_quality_logo_m1.png
; logo file:/MntR.EcolK12_2nt_upstream.25.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161029
; Job done 2019-06-03.161030
; Seconds 0.53
; user 0.53
; system 0.07
; cuser 0.44
; csystem 0.05