RegulonDB
MlrA matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/MlrA/MlrA.EcolK12_1nt_upstream.38.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 /MlrA.EcolK12_1nt_upstream.38.meme_quality_logo
; Input files
; input /MlrA.EcolK12_1nt_upstream.38.meme_quality_matrix.tf
; prior /MlrA.EcolK12_1nt_upstream.38.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /MlrA.EcolK12_1nt_upstream.38.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 1 3 0 2 2 3 4 2 0 0 1 0 3 0 3 1 0 1 2 0 0 1 0 1 1 1 0 0 1 1 3 0 3 2 0 0 0 0
C 2 1 1 0 2 1 0 1 0 0 0 0 1 4 0 0 0 0 0 2 0 1 1 0 0 0 2 0 0 1 0 4 1 1 0 0 0 0
G 0 0 3 2 0 0 0 1 0 0 2 0 0 0 1 1 1 1 1 1 2 0 0 0 1 1 1 0 3 0 1 0 0 0 0 0 0 1
T 1 0 0 0 0 0 0 0 4 4 1 4 0 0 0 2 3 2 1 1 2 2 3 3 2 2 1 4 0 2 0 0 0 1 4 4 4 3
//
A 0.3 0.7 0.1 0.5 0.5 0.7 0.9 0.5 0.1 0.1 0.3 0.1 0.7 0.1 0.7 0.3 0.1 0.3 0.5 0.1 0.1 0.3 0.1 0.3 0.3 0.3 0.1 0.1 0.3 0.3 0.7 0.1 0.7 0.5 0.1 0.1 0.1 0.1
C 0.4 0.2 0.2 0.0 0.4 0.2 0.0 0.2 0.0 0.0 0.0 0.0 0.2 0.8 0.0 0.0 0.0 0.0 0.0 0.4 0.0 0.2 0.2 0.0 0.0 0.0 0.4 0.0 0.0 0.2 0.0 0.8 0.2 0.2 0.0 0.0 0.0 0.0
G 0.0 0.0 0.6 0.4 0.0 0.0 0.0 0.2 0.0 0.0 0.4 0.0 0.0 0.0 0.2 0.2 0.2 0.2 0.2 0.2 0.4 0.0 0.0 0.0 0.2 0.2 0.2 0.0 0.6 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.2
T 0.3 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.9 0.9 0.3 0.9 0.1 0.1 0.1 0.5 0.7 0.5 0.3 0.3 0.5 0.5 0.7 0.7 0.5 0.5 0.3 0.9 0.1 0.5 0.1 0.1 0.1 0.3 0.9 0.9 0.9 0.7
//
A -0.1 0.8 -1.6 0.5 0.5 0.8 1.1 0.5 -1.6 -1.6 -0.1 -1.6 0.8 -1.6 0.8 -0.1 -1.6 -0.1 0.5 -1.6 -1.6 -0.1 -1.6 -0.1 -0.1 -0.1 -1.6 -1.6 -0.1 -0.1 0.8 -1.6 0.8 0.5 -1.6 -1.6 -1.6 -1.6
C 0.8 0.2 0.2 -1.6 0.8 0.2 -1.6 0.2 -1.6 -1.6 -1.6 -1.6 0.2 1.4 -1.6 -1.6 -1.6 -1.6 -1.6 0.8 -1.6 0.2 0.2 -1.6 -1.6 -1.6 0.8 -1.6 -1.6 0.2 -1.6 1.4 0.2 0.2 -1.6 -1.6 -1.6 -1.6
G -1.6 -1.6 1.1 0.8 -1.6 -1.6 -1.6 0.2 -1.6 -1.6 0.8 -1.6 -1.6 -1.6 0.2 0.2 0.2 0.2 0.2 0.2 0.8 -1.6 -1.6 -1.6 0.2 0.2 0.2 -1.6 1.1 -1.6 0.2 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 0.2
T -0.1 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 1.1 1.1 -0.1 1.1 -1.6 -1.6 -1.6 0.4 0.8 0.4 -0.1 -0.1 0.4 0.4 0.8 0.8 0.4 0.4 -0.1 1.1 -1.6 0.4 -1.6 -1.6 -1.6 -0.1 1.1 1.1 1.1 0.8
//
A -0.0 0.5 -0.1 0.2 0.2 0.5 0.9 0.2 -0.1 -0.1 -0.0 -0.1 0.5 -0.1 0.5 -0.0 -0.1 -0.0 0.2 -0.1 -0.1 -0.0 -0.1 -0.0 -0.0 -0.0 -0.1 -0.1 -0.0 -0.0 0.5 -0.1 0.5 0.2 -0.1 -0.1 -0.1 -0.1
C 0.3 0.0 0.0 -0.1 0.3 0.0 -0.1 0.0 -0.1 -0.1 -0.1 -0.1 0.0 1.2 -0.1 -0.1 -0.1 -0.1 -0.1 0.3 -0.1 0.0 0.0 -0.1 -0.1 -0.1 0.3 -0.1 -0.1 0.0 -0.1 1.2 0.0 0.0 -0.1 -0.1 -0.1 -0.1
G -0.1 -0.1 0.7 0.3 -0.1 -0.1 -0.1 0.0 -0.1 -0.1 0.3 -0.1 -0.1 -0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.3 -0.1 -0.1 -0.1 0.0 0.0 0.0 -0.1 0.7 -0.1 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.0
T -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.9 0.9 -0.0 0.9 -0.1 -0.1 -0.1 0.2 0.5 0.2 -0.0 -0.0 0.2 0.2 0.5 0.5 0.2 0.2 -0.0 0.9 -0.1 0.2 -0.1 -0.1 -0.1 -0.0 0.9 0.9 0.9 0.5
//
; Sites 4
>site_0
TAGAAAAGTTGTACATTTGGTTTTTATTGCACAATTTT
>site_1
AACACAACTTGTACGGTAACGTTTATCTGTGCCATTTT
>site_2
CCGGACAATTTTCCATGGATTATTTTCTGAACATTTTT
>site_3
CAGGCAAATTATACAATTTCGCCAGGGTATACACTTTG
;
; Matrix parameters
; Number of sites 4
; Columns 38
; 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 HAGRMAAVTTDTACADTDDBKHTTDDBTGHACAHTTTT
; AC HAGRMAAVTTDTACADTDDBKHTTDDBTGHACAHTTTT
; id HAGRMAAVTTDTACADTDDBKHTTDDBTGHACAHTTTT
; name HAGRMAAVTTDTACADTDDBKHTTDDBTGHACAHTTTT
; description cmSrmmAvTTgTmCrkkkrskyytkksTGyrCmmTTTk
; statistical_basis 4 sequences
; sites 4
; nb_sites 4
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 15.8873
; information.per.column 0.418087
; max.possible.info.per.col 1.58873
; consensus.strict caGgcaAaTTgTaCatttacgtttttcTGtaCaaTTTt
; consensus.strict.rc AAAATTGTACAGAAAAACGTAAATGTACAATTTGCCTG
; consensus.IUPAC cmSrmmAvTTgTmCrkkkrskyytkksTGyrCmmTTTk
; consensus.IUPAC.rc MAAAKKGYRCASMMARRMSYMMMYGKACAABTKKYSKG
; consensus.regexp c[ac][CG][ag][ac][ac]A[acg]TTgT[ac]C[ag][gt][gt][gt][ag][cg][gt][ct][ct]t[gt][gt][cg]TG[ct][ag]C[ac][ac]TTT[gt]
; consensus.regexp.rc [AC]AAA[GT][GT]G[CT][AG]CA[CG][AC][AC]A[AG][AG][AC][CG][CT][AC][AC][AC][CT]G[GT]ACAA[CGT]T[GT][GT][CT][CG][GT]G
; residues.content.crude.freq a:0.2763|c:0.1711|g:0.1579|t:0.3947
; G+C.content.crude.freq 0.328947
; residues.content.corrected.freq a:0.2792|c:0.1784|g:0.1672|t:0.3753
; G+C.content.corrected.freq 0.345507
; min(P(S|M)) 8.65197e-53
; max(P(S|M)) 4.40286e-09
; proba_range 4.40286e-09
; Wmin -61.2
; Wmax 31
; Wrange 92.2
; logo file:/MlrA.EcolK12_1nt_upstream.38.meme_quality_logo_m1.png
; logo file:/MlrA.EcolK12_1nt_upstream.38.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161014
; Job done 2019-06-03.161015
; Seconds 0.61
; user 0.61
; system 0.06
; cuser 0.45
; csystem 0.04