RegulonDB
MetR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/MetR/MetR.EcolK12_2nt_upstream.18.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 /MetR.EcolK12_2nt_upstream.18.meme_quality_logo
; Input files
; input /MetR.EcolK12_2nt_upstream.18.meme_quality_matrix.tf
; prior /MetR.EcolK12_2nt_upstream.18.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /MetR.EcolK12_2nt_upstream.18.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 3 0 0 4 5 3 4 2 2 1 1 0 0 3 0 0 0
C 3 1 0 0 1 0 1 0 0 1 1 1 0 5 1 3 0 0
G 2 0 0 5 0 0 0 1 1 0 0 0 1 0 1 1 1 0
T 0 1 5 0 0 0 1 0 2 2 3 3 4 0 0 1 4 5
//
A 0.0 0.5 0.0 0.0 0.7 0.9 0.5 0.7 0.4 0.4 0.2 0.2 0.0 0.0 0.5 0.0 0.0 0.0
C 0.5 0.2 0.0 0.0 0.2 0.0 0.2 0.0 0.0 0.2 0.2 0.2 0.0 0.9 0.2 0.5 0.0 0.0
G 0.4 0.0 0.0 0.9 0.0 0.0 0.0 0.2 0.2 0.0 0.0 0.0 0.2 0.0 0.2 0.2 0.2 0.0
T 0.0 0.2 0.9 0.0 0.0 0.0 0.2 0.0 0.4 0.4 0.5 0.5 0.7 0.0 0.0 0.2 0.7 0.9
//
A -1.8 0.6 -1.8 -1.8 0.9 1.1 0.6 0.9 0.3 0.3 -0.3 -0.3 -1.8 -1.8 0.6 -1.8 -1.8 -1.8
C 0.9 -0.0 -1.8 -1.8 -0.0 -1.8 -0.0 -1.8 -1.8 -0.0 -0.0 -0.0 -1.8 1.4 -0.0 0.9 -1.8 -1.8
G 0.6 -1.8 -1.8 1.4 -1.8 -1.8 -1.8 -0.0 -0.0 -1.8 -1.8 -1.8 -0.0 -1.8 -0.0 -0.0 -0.0 -1.8
T -1.8 -0.3 1.1 -1.8 -1.8 -1.8 -0.3 -1.8 0.3 0.3 0.6 0.6 0.9 -1.8 -1.8 -0.3 0.9 1.1
//
A -0.1 0.3 -0.1 -0.1 0.6 1.0 0.3 0.6 0.1 0.1 -0.1 -0.1 -0.1 -0.1 0.3 -0.1 -0.1 -0.1
C 0.5 -0.0 -0.1 -0.1 -0.0 -0.1 -0.0 -0.1 -0.1 -0.0 -0.0 -0.0 -0.1 1.2 -0.0 0.5 -0.1 -0.1
G 0.2 -0.1 -0.1 1.3 -0.1 -0.1 -0.1 -0.0 -0.0 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0 -0.0 -0.0 -0.1
T -0.1 -0.1 1.0 -0.1 -0.1 -0.1 -0.1 -0.1 0.1 0.1 0.3 0.3 0.6 -0.1 -0.1 -0.1 0.6 1.0
//
; Sites 5
>site_0
GATGCAAATTTTTCACTT
>site_1
CATGAAAGTCCTTCACTT
>site_2
CATGAATAATTTGCGCTT
>site_3
CCTGAAAAGAAATCCGTT
>site_4
GTTGAACAAATCTCATGT
;
; Matrix parameters
; Number of sites 5
; Columns 18
; 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 SATGAAAADHTTTCACTT
; AC SATGAAAADHTTTCACTT
; id SATGAAAADHTTTCACTT
; name SATGAAAADHTTTCACTT
; description saTGaAaawwtttCactT
; statistical_basis 5 sequences
; sites 5
; nb_sites 5
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 8.46606
; information.per.column 0.470337
; max.possible.info.per.col 1.58952
; consensus.strict caTGaAaaaatttCactT
; consensus.strict.rc AAGTGAAATTTTTTCATG
; consensus.IUPAC saTGaAaawwtttCactT
; consensus.IUPAC.rc AAGTGAAAWWTTTTCATS
; consensus.regexp [cg]aTGaAaa[at][at]tttCactT
; consensus.regexp.rc AAGTGAAA[AT][AT]TTTTCAT[CG]
; residues.content.crude.freq a:0.3111|c:0.2000|g:0.1444|t:0.3444
; G+C.content.crude.freq 0.344444
; residues.content.corrected.freq a:0.3078|c:0.2013|g:0.1544|t:0.3365
; G+C.content.corrected.freq 0.355676
; min(P(S|M)) 1.2007e-26
; max(P(S|M)) 0.000283399
; proba_range 0.000283399
; Wmin -32.3
; Wmax 15.3
; Wrange 47.6
; logo file:/MetR.EcolK12_2nt_upstream.18.meme_quality_logo_m1.png
; logo file:/MetR.EcolK12_2nt_upstream.18.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161014
; Job done 2019-06-03.161015
; Seconds 0.54
; user 0.54
; system 0.05
; cuser 0.43
; csystem 0.04