RegulonDB
PdhR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/PdhR/PdhR.EcolK12_1nt_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 /PdhR.EcolK12_1nt_upstream.19.meme_quality_logo
; Input files
; input /PdhR.EcolK12_1nt_upstream.19.meme_quality_matrix.tf
; prior /PdhR.EcolK12_1nt_upstream.19.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /PdhR.EcolK12_1nt_upstream.19.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 4 9 0 0 1 1 1 3 4 3 9 0 3 9 5 1 3 1
C 5 1 0 2 2 0 0 1 4 0 1 0 8 6 0 0 1 0 0
G 2 1 0 0 0 8 8 0 1 0 2 0 1 0 0 1 0 2 0
T 2 3 0 7 7 0 0 7 1 5 3 0 0 0 0 3 7 4 8
//
A 0.0 0.4 0.9 0.0 0.0 0.1 0.1 0.1 0.3 0.4 0.3 0.9 0.0 0.3 0.9 0.5 0.1 0.3 0.1
C 0.5 0.1 0.0 0.2 0.2 0.0 0.0 0.1 0.4 0.0 0.1 0.0 0.8 0.6 0.0 0.0 0.1 0.0 0.0
G 0.2 0.1 0.0 0.0 0.0 0.8 0.8 0.0 0.1 0.0 0.2 0.0 0.1 0.0 0.0 0.1 0.0 0.2 0.0
T 0.2 0.3 0.0 0.7 0.7 0.0 0.0 0.7 0.1 0.5 0.3 0.0 0.0 0.0 0.0 0.3 0.7 0.4 0.8
//
A -2.3 0.4 1.2 -2.3 -2.3 -0.8 -0.8 -0.8 0.1 0.4 0.1 1.2 -2.3 0.1 1.2 0.6 -0.8 0.1 -0.8
C 0.9 -0.5 -2.3 0.1 0.1 -2.3 -2.3 -0.5 0.7 -2.3 -0.5 -2.3 1.4 1.1 -2.3 -2.3 -0.5 -2.3 -2.3
G 0.1 -0.5 -2.3 -2.3 -2.3 1.4 1.4 -2.3 -0.5 -2.3 0.1 -2.3 -0.5 -2.3 -2.3 -0.5 -2.3 0.1 -2.3
T -0.3 0.1 -2.3 0.9 0.9 -2.3 -2.3 0.9 -0.8 0.6 0.1 -2.3 -2.3 -2.3 -2.3 0.1 0.9 0.4 1.0
//
A -0.1 0.2 1.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.0 0.2 0.0 1.1 -0.1 0.0 1.1 0.3 -0.1 0.0 -0.1
C 0.5 -0.1 -0.0 0.0 0.0 -0.0 -0.0 -0.1 0.3 -0.0 -0.1 -0.0 1.1 0.7 -0.0 -0.0 -0.1 -0.0 -0.0
G 0.0 -0.1 -0.0 -0.0 -0.0 1.1 1.1 -0.0 -0.1 -0.0 0.0 -0.0 -0.1 -0.0 -0.0 -0.1 -0.0 0.0 -0.0
T -0.1 0.0 -0.1 0.7 0.7 -0.1 -0.1 0.7 -0.1 0.3 0.0 -0.1 -0.1 -0.1 -0.1 0.0 0.7 0.2 0.9
//
; Sites 9
>site_0
CAATTGGTCTTACCAATTT
>site_1
CAATTGGTATAACCAATGT
>site_2
CAATTGGTAAAACCATTGT
>site_3
CTACCGGTCAGACCATTTT
>site_4
GCATTGGTCATACCAAAAT
>site_5
TTATTGGTCATACAAATAA
>site_6
GTATTAGTGTCACCAATTT
>site_7
CAATCGAAATAAGAATTAT
>site_8
TGACTGGCTTGACAAGCTT
;
; Matrix parameters
; Number of sites 9
; Columns 19
; 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 CWATTGGTMWDACMAWTDT
; AC CWATTGGTMWDACMAWTDT
; id CWATTGGTMWDACMAWTDT
; name CWATTGGTMWDACMAWTDT
; description swAyyGGtmwdACMAwtdT
; statistical_basis 9 sequences
; sites 9
; nb_sites 9
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 10.1773
; information.per.column 0.535647
; max.possible.info.per.col 1.58873
; consensus.strict caAttGGtctaACCAattT
; consensus.strict.rc AAATTGGTTAGACCAATTG
; consensus.IUPAC swAyyGGtmwdACMAwtdT
; consensus.IUPAC.rc AHAWTKGTHWKACCRRTWS
; consensus.regexp [cg][at]A[ct][ct]GGt[ac][at][agt]AC[AC]A[at]t[agt]T
; consensus.regexp.rc A[ACT]A[AT]T[GT]GT[ACT][AT][GT]ACC[AG][AG]T[AT][CG]
; residues.content.crude.freq a:0.3333|c:0.1813|g:0.1520|t:0.3333
; G+C.content.crude.freq 0.333333
; residues.content.corrected.freq a:0.3291|c:0.1839|g:0.1573|t:0.3297
; G+C.content.corrected.freq 0.341175
; min(P(S|M)) 3.46486e-30
; max(P(S|M)) 0.000241624
; proba_range 0.000241624
; Wmin -38.8
; Wmax 17.1
; Wrange 55.9
; logo file:/PdhR.EcolK12_1nt_upstream.19.meme_quality_logo_m1.png
; logo file:/PdhR.EcolK12_1nt_upstream.19.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161100
; Seconds 0.55
; user 0.56
; system 0.05
; cuser 0.41
; csystem 0.04