RegulonDB
PuuR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/PuuR/PuuR.EcolK12_1nt_upstream.22.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 /PuuR.EcolK12_1nt_upstream.22.meme_quality_logo
; Input files
; input /PuuR.EcolK12_1nt_upstream.22.meme_quality_matrix.tf
; prior /PuuR.EcolK12_1nt_upstream.22.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /PuuR.EcolK12_1nt_upstream.22.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 3 3 2 2 0 0 0 4 3 3 4 2 4 0 3 3 0 0 3 2 0 4
C 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 2 4 0
G 0 1 1 2 0 3 3 0 0 0 0 0 0 0 0 0 0 3 1 0 0 0
T 1 0 0 0 3 1 1 0 0 1 0 2 0 4 1 1 4 0 0 0 0 0
//
A 0.7 0.7 0.5 0.5 0.1 0.1 0.1 0.9 0.7 0.7 0.9 0.5 0.9 0.1 0.7 0.7 0.1 0.1 0.7 0.5 0.1 0.9
C 0.0 0.0 0.2 0.0 0.2 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.4 0.8 0.0
G 0.0 0.2 0.2 0.4 0.0 0.6 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.6 0.2 0.0 0.0 0.0
T 0.3 0.1 0.1 0.1 0.7 0.3 0.3 0.1 0.1 0.3 0.1 0.5 0.1 0.9 0.3 0.3 0.9 0.1 0.1 0.1 0.1 0.1
//
A 0.8 0.8 0.5 0.5 -1.6 -1.6 -1.6 1.1 0.8 0.8 1.1 0.5 1.1 -1.6 0.8 0.8 -1.6 -1.6 0.8 0.5 -1.6 1.1
C -1.6 -1.6 0.2 -1.6 0.2 -1.6 -1.6 -1.6 0.2 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 0.2 -1.6 0.8 1.4 -1.6
G -1.6 0.2 0.2 0.8 -1.6 1.1 1.1 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 1.1 0.2 -1.6 -1.6 -1.6
T -0.1 -1.6 -1.6 -1.6 0.8 -0.1 -0.1 -1.6 -1.6 -0.1 -1.6 0.4 -1.6 1.1 -0.1 -0.1 1.1 -1.6 -1.6 -1.6 -1.6 -1.6
//
A 0.5 0.5 0.2 0.2 -0.1 -0.1 -0.1 0.9 0.5 0.5 0.9 0.2 0.9 -0.1 0.5 0.5 -0.1 -0.1 0.5 0.2 -0.1 0.9
C -0.1 -0.1 0.0 -0.1 0.0 -0.1 -0.1 -0.1 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.0 -0.1 0.3 1.2 -0.1
G -0.1 0.0 0.0 0.3 -0.1 0.7 0.7 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.7 0.0 -0.1 -0.1 -0.1
T -0.0 -0.1 -0.1 -0.1 0.5 -0.0 -0.0 -0.1 -0.1 -0.0 -0.1 0.2 -0.1 0.9 -0.0 -0.0 0.9 -0.1 -0.1 -0.1 -0.1 -0.1
//
; Sites 4
>site_0
AGCATGGAAAATATAATGAACA
>site_1
AAAGCGTAAAATATAATGACCA
>site_2
AAAGTGGACTAAATTATCGCCA
>site_3
TAGATTGAAAAAATATTGAACA
;
; Matrix parameters
; Number of sites 4
; Columns 22
; 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 AAVRTGGAAAAWATAATGAMCA
; AC AAVRTGGAAAAWATAATGAMCA
; id AAVRTGGAAAAWATAATGAMCA
; name AAVRTGGAAAAWATAATGAMCA
; description arvryGGAmaAwATaaTSrmCA
; statistical_basis 4 sequences
; sites 4
; nb_sites 4
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 11.1012
; information.per.column 0.5046
; max.possible.info.per.col 1.58873
; consensus.strict aaagtGGAaaAaATaaTGacCA
; consensus.strict.rc TGGTCATTATTTTTTCCACTTT
; consensus.IUPAC arvryGGAmaAwATaaTSrmCA
; consensus.IUPAC.rc TGKYSATTATWTTKTCCRYBYT
; consensus.regexp a[ag][acg][ag][ct]GGA[ac]aA[at]ATaaT[CG][ag][ac]CA
; consensus.regexp.rc TG[GT][CT][CG]ATTAT[AT]TT[GT]TCC[AG][CT][CGT][CT]T
; residues.content.crude.freq a:0.5114|c:0.1136|g:0.1591|t:0.2159
; G+C.content.crude.freq 0.272727
; residues.content.corrected.freq a:0.4673|c:0.1324|g:0.1681|t:0.2322
; G+C.content.corrected.freq 0.300531
; min(P(S|M)) 6.24823e-31
; max(P(S|M)) 0.000138387
; proba_range 0.000138387
; Wmin -35.5
; Wmax 20.3
; Wrange 55.8
; logo file:/PuuR.EcolK12_1nt_upstream.22.meme_quality_logo_m1.png
; logo file:/PuuR.EcolK12_1nt_upstream.22.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161100
; Seconds 0.63
; user 0.63
; system 0.05
; cuser 0.43
; csystem 0.04