RegulonDB
MetJ matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/MetJ/MetJ.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 /MetJ.EcolK12_2nt_upstream.19.meme_quality_logo
; Input files
; input /MetJ.EcolK12_2nt_upstream.19.meme_quality_matrix.tf
; prior /MetJ.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 /MetJ.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 7 1 14 1 4 0 3 4 11 5 13 1 6 2 4 1 4 4 12
C 0 0 0 9 0 0 10 2 0 3 0 8 0 1 8 2 0 2 1
G 7 13 0 0 11 3 0 1 3 4 1 1 6 2 2 3 5 4 1
T 1 1 1 5 0 12 2 8 1 3 1 5 3 10 1 9 6 5 1
//
A 0.5 0.1 0.9 0.1 0.3 0.0 0.2 0.3 0.7 0.3 0.8 0.1 0.4 0.1 0.3 0.1 0.3 0.3 0.8
C 0.0 0.0 0.0 0.6 0.0 0.0 0.6 0.1 0.0 0.2 0.0 0.5 0.0 0.1 0.5 0.1 0.0 0.1 0.1
G 0.5 0.8 0.0 0.0 0.7 0.2 0.0 0.1 0.2 0.3 0.1 0.1 0.4 0.1 0.1 0.2 0.3 0.3 0.1
T 0.1 0.1 0.1 0.3 0.0 0.8 0.1 0.5 0.1 0.2 0.1 0.3 0.2 0.6 0.1 0.6 0.4 0.3 0.1
//
A 0.4 -1.3 1.1 -1.3 -0.1 -2.8 -0.3 -0.1 0.9 0.1 1.0 -1.3 0.3 -0.7 -0.1 -1.3 -0.1 -0.1 1.0
C -2.8 -2.8 -2.8 1.0 -2.8 -2.8 1.1 -0.4 -2.8 -0.0 -2.8 0.9 -2.8 -1.0 0.9 -0.4 -2.8 -0.4 -1.0
G 0.8 1.4 -2.8 -2.8 1.2 -0.0 -2.8 -1.0 -0.0 0.3 -1.0 -1.0 0.6 -0.4 -0.4 -0.0 0.5 0.3 -1.0
T -1.3 -1.3 -1.3 0.1 -2.8 1.0 -0.7 0.6 -1.3 -0.4 -1.3 0.1 -0.4 0.8 -1.3 0.7 0.3 0.1 -1.3
//
A 0.2 -0.1 1.0 -0.1 -0.0 -0.1 -0.1 -0.0 0.6 0.0 0.9 -0.1 0.1 -0.1 -0.0 -0.1 -0.0 -0.0 0.7
C -0.0 -0.0 -0.0 0.6 -0.0 -0.0 0.7 -0.1 -0.0 -0.0 -0.0 0.5 -0.0 -0.1 0.5 -0.1 -0.0 -0.1 -0.1
G 0.4 1.2 -0.0 -0.0 0.9 -0.0 -0.0 -0.1 -0.0 0.1 -0.1 -0.1 0.2 -0.1 -0.1 -0.0 0.2 0.1 -0.1
T -0.1 -0.1 -0.1 0.0 -0.1 0.7 -0.1 0.3 -0.1 -0.1 -0.1 0.0 -0.1 0.5 -0.1 0.4 0.1 0.0 -0.1
//
; Sites 15
>site_0
GGACGTCAATACATCTGGA
>site_1
GGACGTCTAAACGGATAGA
>site_2
AGACGTCTGGATGCCTTAA
>site_3
GGACATCTAAACTTCTTTG
>site_4
AGACATCCAGATAGCTGAA
>site_5
AGATGTTAAAACATCGTTA
>site_6
AGACGTCCAGATGTAAAGA
>site_7
AGATGTTTACACATCCATA
>site_8
GGATGGATTAACATCTGGA
>site_9
GGACATCTATACTTCCTCC
>site_10
AGATGTAAAGATGAAGGAA
>site_11
AAACGTATAAGCGTATGTA
>site_12
GGATGGCTATTTTAGGTCA
>site_13
GGAAGGCGGCAAGTTTATT
>site_14
TTTCATCAGCAGATGTTAA
;
; Matrix parameters
; Number of sites 15
; 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 RGAYGTCWANAYDTMTDDA
; AC RGAYGTCWANAYDTMTDDA
; id RGAYGTCWANAYDTMTDDA
; name RGAYGTCWANAYDTMTDDA
; description rGAYGtCtarAyrtctkka
; statistical_basis 15 sequences
; sites 15
; nb_sites 15
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 7.89765
; information.per.column 0.415666
; max.possible.info.per.col 1.58952
; consensus.strict gGACGtCtagAcgtctgga
; consensus.strict.rc TCCAGACGTCTAGACGTCC
; consensus.IUPAC rGAYGtCtarAyrtctkka
; consensus.IUPAC.rc TMMAGAYRTYTAGACRTCY
; consensus.regexp [ag]GA[CT]GtCta[ag]A[ct][ag]tct[gt][gt]a
; consensus.regexp.rc T[AC][AC]AGA[CT][AG]T[CT]TAGAC[AG]TC[CT]
; residues.content.crude.freq a:0.3404|c:0.1614|g:0.2351|t:0.2632
; G+C.content.crude.freq 0.396491
; residues.content.corrected.freq a:0.3373|c:0.1643|g:0.2331|t:0.2653
; G+C.content.corrected.freq 0.39745
; min(P(S|M)) 9.77472e-30
; max(P(S|M)) 2.58418e-05
; proba_range 2.58418e-05
; Wmin -38.5
; Wmax 16
; Wrange 54.5
; logo file:/MetJ.EcolK12_2nt_upstream.19.meme_quality_logo_m1.png
; logo file:/MetJ.EcolK12_2nt_upstream.19.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161014
; Job done 2019-06-03.161015
; Seconds 0.55
; user 0.55
; system 0.04
; cuser 0.43
; csystem 0.05