RegulonDB
MelR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/MelR/MelR.EcolK12_2nt_upstream.21.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 /MelR.EcolK12_2nt_upstream.21.meme_quality_logo
; Input files
; input /MelR.EcolK12_2nt_upstream.21.meme_quality_matrix.tf
; prior /MelR.EcolK12_2nt_upstream.21.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /MelR.EcolK12_2nt_upstream.21.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 3 0 1 2 0 0 2 0 4 5 4 2 0 0 4 0 5 1 0 0 2
C 0 1 0 3 5 4 0 0 0 0 0 2 1 5 0 0 0 0 1 1 0
G 0 0 0 0 0 0 1 3 1 0 0 1 1 0 1 5 0 2 1 0 0
T 2 4 4 0 0 1 2 2 0 0 1 0 3 0 0 0 0 2 3 4 3
//
A 0.5 0.0 0.2 0.4 0.0 0.0 0.4 0.0 0.7 0.9 0.7 0.4 0.0 0.0 0.7 0.0 0.9 0.2 0.0 0.0 0.4
C 0.0 0.2 0.0 0.5 0.9 0.7 0.0 0.0 0.0 0.0 0.0 0.4 0.2 0.9 0.0 0.0 0.0 0.0 0.2 0.2 0.0
G 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.5 0.2 0.0 0.0 0.2 0.2 0.0 0.2 0.9 0.0 0.4 0.2 0.0 0.0
T 0.4 0.7 0.7 0.0 0.0 0.2 0.4 0.4 0.0 0.0 0.2 0.0 0.5 0.0 0.0 0.0 0.0 0.4 0.5 0.7 0.5
//
A 0.6 -1.8 -0.3 0.3 -1.8 -1.8 0.3 -1.8 0.9 1.1 0.9 0.3 -1.8 -1.8 0.9 -1.8 1.1 -0.3 -1.8 -1.8 0.3
C -1.8 -0.0 -1.8 0.9 1.4 1.2 -1.8 -1.8 -1.8 -1.8 -1.8 0.6 -0.0 1.4 -1.8 -1.8 -1.8 -1.8 -0.0 -0.0 -1.8
G -1.8 -1.8 -1.8 -1.8 -1.8 -1.8 -0.0 1.0 -0.0 -1.8 -1.8 -0.0 -0.0 -1.8 -0.0 1.4 -1.8 0.6 -0.0 -1.8 -1.8
T 0.3 0.9 0.9 -1.8 -1.8 -0.3 0.3 0.3 -1.8 -1.8 -0.3 -1.8 0.6 -1.8 -1.8 -1.8 -1.8 0.3 0.6 0.9 0.6
//
A 0.3 -0.1 -0.1 0.1 -0.1 -0.1 0.1 -0.1 0.6 1.0 0.6 0.1 -0.1 -0.1 0.6 -0.1 1.0 -0.1 -0.1 -0.1 0.1
C -0.1 -0.0 -0.1 0.5 1.2 0.9 -0.1 -0.1 -0.1 -0.1 -0.1 0.2 -0.0 1.2 -0.1 -0.1 -0.1 -0.1 -0.0 -0.0 -0.1
G -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 0.5 -0.0 -0.1 -0.1 -0.0 -0.0 -0.1 -0.0 1.3 -0.1 0.2 -0.0 -0.1 -0.1
T 0.1 0.6 0.6 -0.1 -0.1 -0.1 0.1 0.1 -0.1 -0.1 -0.1 -0.1 0.3 -0.1 -0.1 -0.1 -0.1 0.1 0.3 0.6 0.3
//
; Sites 5
>site_0
ATTCCCATAAACTCAGATTTA
>site_1
ATTACCTGAAAAGCAGAGTTT
>site_2
ATTCCCATAAACTCAGATCCT
>site_3
TTTCCTGGAATATCAGAATTA
>site_4
TCAACCTGGAAGCCGGAGGTT
;
; Matrix parameters
; Number of sites 5
; Columns 21
; 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 WTTMCCDKAAAVTCAGADTTW
; AC WTTMCCDKAAAVTCAGADTTW
; id WTTMCCDKAAAVTCAGADTTW
; name WTTMCCDKAAAVTCAGADTTW
; description wttmCCwkaAamtCaGAkttw
; statistical_basis 5 sequences
; sites 5
; nb_sites 5
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 10.6038
; information.per.column 0.504941
; max.possible.info.per.col 1.58952
; consensus.strict attcCCagaAactCaGAgttt
; consensus.strict.rc AAACTCTGAGTTTCTGGGAAT
; consensus.IUPAC wttmCCwkaAamtCaGAkttw
; consensus.IUPAC.rc WAAMTCTGAKTTTMWGGKAAW
; consensus.regexp [at]tt[ac]CC[at][gt]aAa[ac]tCaGA[gt]tt[at]
; consensus.regexp.rc [AT]AA[AC]TCTGA[GT]TTT[AC][AT]GG[GT]AA[AT]
; residues.content.crude.freq a:0.3333|c:0.2190|g:0.1524|t:0.2952
; G+C.content.crude.freq 0.371429
; residues.content.corrected.freq a:0.3263|c:0.2172|g:0.1610|t:0.2955
; G+C.content.corrected.freq 0.378163
; min(P(S|M)) 4.80852e-31
; max(P(S|M)) 6.96385e-05
; proba_range 6.96385e-05
; Wmin -37.7
; Wmax 18.9
; Wrange 56.6
; logo file:/MelR.EcolK12_2nt_upstream.21.meme_quality_logo_m1.png
; logo file:/MelR.EcolK12_2nt_upstream.21.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161014
; Job done 2019-06-03.161015
; Seconds 0.59
; user 0.59
; system 0.05
; cuser 0.38
; csystem 0.03