RegulonDB
QseB matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/QseB/QseB.EcolK12_1nt_upstream.16.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 /QseB.EcolK12_1nt_upstream.16.meme_quality_logo
; Input files
; input /QseB.EcolK12_1nt_upstream.16.meme_quality_matrix.tf
; prior /QseB.EcolK12_1nt_upstream.16.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /QseB.EcolK12_1nt_upstream.16.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 0 1 3 4 1 4 4 1 2 4 2 2 2 1 1 0
C 0 1 0 0 3 0 0 0 0 0 2 1 0 1 0 1
G 4 0 1 0 0 0 0 0 0 0 0 1 2 0 0 0
T 0 2 0 0 0 0 0 3 2 0 0 0 0 2 3 3
//
A 0.1 0.3 0.7 0.9 0.3 0.9 0.9 0.3 0.5 0.9 0.5 0.5 0.5 0.3 0.3 0.1
C 0.0 0.2 0.0 0.0 0.6 0.0 0.0 0.0 0.0 0.0 0.4 0.2 0.0 0.2 0.0 0.2
G 0.8 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.4 0.0 0.0 0.0
T 0.1 0.5 0.1 0.1 0.1 0.1 0.1 0.7 0.5 0.1 0.1 0.1 0.1 0.5 0.7 0.7
//
A -1.6 -0.1 0.8 1.1 -0.1 1.1 1.1 -0.1 0.5 1.1 0.5 0.5 0.5 -0.1 -0.1 -1.6
C -1.6 0.2 -1.6 -1.6 1.1 -1.6 -1.6 -1.6 -1.6 -1.6 0.8 0.2 -1.6 0.2 -1.6 0.2
G 1.4 -1.6 0.2 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 0.2 0.8 -1.6 -1.6 -1.6
T -1.6 0.4 -1.6 -1.6 -1.6 -1.6 -1.6 0.8 0.4 -1.6 -1.6 -1.6 -1.6 0.4 0.8 0.8
//
A -0.1 -0.0 0.5 0.9 -0.0 0.9 0.9 -0.0 0.2 0.9 0.2 0.2 0.2 -0.0 -0.0 -0.1
C -0.1 0.0 -0.1 -0.1 0.7 -0.1 -0.1 -0.1 -0.1 -0.1 0.3 0.0 -0.1 0.0 -0.1 0.0
G 1.2 -0.1 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.0 0.3 -0.1 -0.1 -0.1
T -0.1 0.2 -0.1 -0.1 -0.1 -0.1 -0.1 0.5 0.2 -0.1 -0.1 -0.1 -0.1 0.2 0.5 0.5
//
; Sites 4
>site_0
GTAACAATTACGGATT
>site_1
GTGACAATAACCGCTT
>site_2
GCAACAATAAAAATAC
>site_3
GAAAAAAATAAAATTT
;
; Matrix parameters
; Number of sites 4
; Columns 16
; 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 GHAACAATWAMVRHTT
; AC GHAACAATWAMVRHTT
; id GHAACAATWAMVRHTT
; name GHAACAATWAMVRHTT
; description GyrACAAtwAmvryty
; statistical_basis 4 sequences
; sites 4
; nb_sites 4
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 7.31613
; information.per.column 0.457258
; max.possible.info.per.col 1.58873
; consensus.strict GtaACAAtaAcagttt
; consensus.strict.rc AAACTGTTATTGTTAC
; consensus.IUPAC GyrACAAtwAmvryty
; consensus.IUPAC.rc RARYBKTWATTGTYRC
; consensus.regexp G[ct][ag]ACAAt[at]A[ac][acg][ag][ct]t[ct]
; consensus.regexp.rc [AG]A[AG][CT][CGT][GT]T[AT]ATTGT[CT][AG]C
; residues.content.crude.freq a:0.5000|c:0.1406|g:0.1250|t:0.2344
; G+C.content.crude.freq 0.265625
; residues.content.corrected.freq a:0.4582|c:0.1540|g:0.1408|t:0.2470
; G+C.content.corrected.freq 0.294849
; min(P(S|M)) 9.15015e-23
; max(P(S|M)) 0.000515286
; proba_range 0.000515286
; Wmin -25.8
; Wmax 13.4
; Wrange 39.2
; logo file:/QseB.EcolK12_1nt_upstream.16.meme_quality_logo_m1.png
; logo file:/QseB.EcolK12_1nt_upstream.16.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161100
; Seconds 0.6
; user 0.6
; system 0.05
; cuser 0.41
; csystem 0.05