RegulonDB
MqsA matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/MqsA/MqsA.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 /MqsA.EcolK12_2nt_upstream.21.meme_quality_logo
; Input files
; input /MqsA.EcolK12_2nt_upstream.21.meme_quality_matrix.tf
; prior /MqsA.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 /MqsA.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 2 4 2 3 6 0 0 1 3 5 3 5 0 0 2 1 4 1 1 1 4
C 0 2 2 2 0 6 4 0 0 0 2 0 0 0 0 1 1 2 0 0 0
G 1 0 1 1 0 0 1 0 0 1 1 1 5 4 0 1 1 3 0 0 0
T 3 0 1 0 0 0 1 5 3 0 0 0 1 2 4 3 0 0 5 5 2
//
A 0.3 0.6 0.3 0.5 0.9 0.0 0.0 0.2 0.5 0.8 0.5 0.8 0.0 0.0 0.3 0.2 0.6 0.2 0.2 0.2 0.6
C 0.0 0.3 0.3 0.3 0.0 0.9 0.6 0.0 0.0 0.0 0.3 0.0 0.0 0.0 0.0 0.2 0.2 0.3 0.0 0.0 0.0
G 0.2 0.0 0.2 0.2 0.0 0.0 0.2 0.0 0.0 0.2 0.2 0.2 0.7 0.6 0.0 0.2 0.2 0.5 0.0 0.0 0.0
T 0.5 0.0 0.2 0.0 0.0 0.0 0.2 0.8 0.5 0.0 0.0 0.0 0.2 0.3 0.6 0.5 0.0 0.0 0.8 0.8 0.3
//
A 0.1 0.7 0.1 0.5 1.1 -1.9 -1.9 -0.5 0.5 1.0 0.5 1.0 -1.9 -1.9 0.1 -0.5 0.7 -0.5 -0.5 -0.5 0.7
C -1.9 0.4 0.4 0.4 -1.9 1.5 1.1 -1.9 -1.9 -1.9 0.4 -1.9 -1.9 -1.9 -1.9 -0.2 -0.2 0.4 -1.9 -1.9 -1.9
G -0.2 -1.9 -0.2 -0.2 -1.9 -1.9 -0.2 -1.9 -1.9 -0.2 -0.2 -0.2 1.3 1.1 -1.9 -0.2 -0.2 0.8 -1.9 -1.9 -1.9
T 0.5 -1.9 -0.5 -1.9 -1.9 -1.9 -0.5 0.9 0.5 -1.9 -1.9 -1.9 -0.5 0.1 0.7 0.5 -1.9 -1.9 0.9 0.9 0.1
//
A 0.0 0.5 0.0 0.2 1.0 -0.1 -0.1 -0.1 0.2 0.7 0.2 0.7 -0.1 -0.1 0.0 -0.1 0.5 -0.1 -0.1 -0.1 0.5
C -0.1 0.1 0.1 0.1 -0.1 1.3 0.6 -0.1 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.0 0.1 -0.1 -0.1 -0.1
G -0.0 -0.1 -0.0 -0.0 -0.1 -0.1 -0.0 -0.1 -0.1 -0.0 -0.0 -0.0 1.0 0.6 -0.1 -0.0 -0.0 0.4 -0.1 -0.1 -0.1
T 0.2 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.7 0.2 -0.1 -0.1 -0.1 -0.1 0.0 0.4 0.2 -0.1 -0.1 0.7 0.7 0.0
//
; Sites 6
>site_0
AAGCACCTAAAAGGTTAGTTA
>site_1
TATAACCTAAAAGGTTAATTA
>site_2
TCAGACCTTGCAGGTGGGTAA
>site_3
TAAAACCTTAAGGTTAACATT
>site_4
AACCACTTAACAGTACCCTTT
>site_5
GCCAACGATAGATGATAGTTA
;
; Matrix parameters
; Number of sites 6
; 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 WMNMACCTWAMAGKWTASTTW
; AC WMNMACCTWAMAGKWTASTTW
; id WMNMACCTWAMAGKWTASTTW
; name WMNMACCTWAMAGKWTASTTW
; description wmmmACCtwamaGKwtasttw
; statistical_basis 6 sequences
; sites 6
; nb_sites 6
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 9.18171
; information.per.column 0.437224
; max.possible.info.per.col 1.58952
; consensus.strict tacaACCtaaaaGGttagtta
; consensus.strict.rc TAACTAACCTTTTAGGTTGTA
; consensus.IUPAC wmmmACCtwamaGKwtasttw
; consensus.IUPAC.rc WAASTAWMCTKTWAGGTKKKW
; consensus.regexp [at][ac][ac][ac]ACCt[at]a[ac]aG[GT][at]ta[cg]tt[at]
; consensus.regexp.rc [AT]AA[CG]TA[AT][AC]CT[GT]T[AT]AGGT[GT][GT][GT][AT]
; residues.content.crude.freq a:0.3810|c:0.1746|g:0.1667|t:0.2778
; G+C.content.crude.freq 0.34127
; residues.content.corrected.freq a:0.3681|c:0.1793|g:0.1720|t:0.2805
; G+C.content.corrected.freq 0.351351
; min(P(S|M)) 1.39618e-30
; max(P(S|M)) 2.59154e-05
; proba_range 2.59154e-05
; Wmin -38
; Wmax 17.3
; Wrange 55.3
; logo file:/MqsA.EcolK12_2nt_upstream.21.meme_quality_logo_m1.png
; logo file:/MqsA.EcolK12_2nt_upstream.21.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161029
; Job done 2019-06-03.161030
; Seconds 0.57
; user 0.57
; system 0.04
; cuser 0.42
; csystem 0.05