RegulonDB
BasR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/BasR/BasR.EcolK12_1nt_upstream.23.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 /BasR.EcolK12_1nt_upstream.23.meme_quality_logo
; Input files
; input /BasR.EcolK12_1nt_upstream.23.meme_quality_matrix.tf
; prior /BasR.EcolK12_1nt_upstream.23.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /BasR.EcolK12_1nt_upstream.23.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 0 5 4 1 2 0 0 8 8 1 2 2 0 2 2 4 0 0 5 8 2 1
C 2 0 2 3 4 6 0 0 0 0 1 0 0 0 0 1 3 0 0 1 0 0 1
G 1 5 0 0 1 0 0 0 0 0 5 5 1 2 0 1 1 2 2 2 0 4 2
T 5 3 1 1 2 0 8 8 0 0 1 1 5 6 6 4 0 6 6 0 0 2 4
//
A 0.0 0.0 0.6 0.5 0.1 0.3 0.0 0.0 0.9 0.9 0.1 0.3 0.3 0.0 0.3 0.3 0.5 0.0 0.0 0.6 0.9 0.3 0.1
C 0.2 0.0 0.2 0.4 0.5 0.7 0.0 0.0 0.0 0.0 0.1 0.0 0.0 0.0 0.0 0.1 0.4 0.0 0.0 0.1 0.0 0.0 0.1
G 0.1 0.6 0.0 0.0 0.1 0.0 0.0 0.0 0.0 0.0 0.6 0.6 0.1 0.2 0.0 0.1 0.1 0.2 0.2 0.2 0.0 0.5 0.2
T 0.6 0.4 0.1 0.1 0.3 0.0 0.9 0.9 0.0 0.0 0.1 0.1 0.6 0.7 0.7 0.5 0.0 0.7 0.7 0.0 0.0 0.3 0.5
//
A -2.2 -2.2 0.7 0.5 -0.7 -0.1 -2.2 -2.2 1.2 1.2 -0.7 -0.1 -0.1 -2.2 -0.1 -0.1 0.5 -2.2 -2.2 0.7 1.2 -0.1 -0.7
C 0.2 -2.2 0.2 0.5 0.8 1.2 -2.2 -2.2 -2.2 -2.2 -0.4 -2.2 -2.2 -2.2 -2.2 -0.4 0.5 -2.2 -2.2 -0.4 -2.2 -2.2 -0.4
G -0.4 1.0 -2.2 -2.2 -0.4 -2.2 -2.2 -2.2 -2.2 -2.2 1.0 1.0 -0.4 0.2 -2.2 -0.4 -0.4 0.2 0.2 0.2 -2.2 0.8 0.2
T 0.7 0.2 -0.7 -0.7 -0.2 -2.2 1.1 1.1 -2.2 -2.2 -0.7 -0.7 0.7 0.9 0.9 0.5 -2.2 0.9 0.9 -2.2 -2.2 -0.2 0.5
//
A -0.1 -0.1 0.4 0.2 -0.1 -0.0 -0.1 -0.1 1.1 1.1 -0.1 -0.0 -0.0 -0.1 -0.0 -0.0 0.2 -0.1 -0.1 0.4 1.1 -0.0 -0.1
C 0.0 -0.1 0.0 0.2 0.4 0.8 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.2 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
G -0.1 0.6 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0 -0.0 0.6 0.6 -0.1 0.0 -0.0 -0.1 -0.1 0.0 0.0 0.0 -0.0 0.4 0.0
T 0.4 0.1 -0.1 -0.1 -0.0 -0.1 1.0 1.0 -0.1 -0.1 -0.1 -0.1 0.4 0.6 0.6 0.2 -0.1 0.6 0.6 -0.1 -0.1 -0.0 0.2
//
; Sites 8
>site_0
TTAACCTTAAGGTTTTATTAAGT
>site_1
TGCCTCTTAAGGTTTTCTTAAGG
>site_2
TTACCCTTAAGATTTCAGGAATT
>site_3
TTTCCCTTAAGAAGTTGTTAAGG
>site_4
CGAACATTAAGGAGTAATTGAAC
>site_5
TGCAACTTAACGTTATCGTGAAA
>site_6
CGAATATTAAATTTTGCTGAATT
>site_7
GGATGCTTAATGGTAAATTCAGT
;
; Matrix parameters
; Number of sites 8
; Columns 23
; 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 TKAMYCTTAAGGTTTWMTTAADK
; AC TKAMYCTTAAGGTTTWMTTAADK
; id TKAMYCTTAAGGTTTWMTTAADK
; name TKAMYCTTAAGGTTTWMTTAADK
; description yKmmcCTTAAGGtkttmkkrAgk
; statistical_basis 8 sequences
; sites 8
; nb_sites 8
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 10.8277
; information.per.column 0.470769
; max.possible.info.per.col 1.58873
; consensus.strict tGaccCTTAAGGttttcttaAgt
; consensus.strict.rc ACTTAAGAAAACCTTAAGGGTCA
; consensus.IUPAC yKmmcCTTAAGGtkttmkkrAgk
; consensus.IUPAC.rc MCTYMMKAAMACCTTAAGGKKMR
; consensus.regexp [ct][GT][ac][ac]cCTTAAGGt[gt]tt[ac][gt][gt][ag]Ag[gt]
; consensus.regexp.rc [AC]CT[CT][AC][AC][GT]AA[AC]ACCTTAAGG[GT][GT][AC][AG]
; residues.content.crude.freq a:0.3098|c:0.1304|g:0.1848|t:0.3750
; G+C.content.crude.freq 0.315217
; residues.content.corrected.freq a:0.3077|c:0.1390|g:0.1869|t:0.3664
; G+C.content.corrected.freq 0.325943
; min(P(S|M)) 6.2821e-35
; max(P(S|M)) 2.87806e-05
; proba_range 2.87806e-05
; Wmin -44.4
; Wmax 20
; Wrange 64.4
; logo file:/BasR.EcolK12_1nt_upstream.23.meme_quality_logo_m1.png
; logo file:/BasR.EcolK12_1nt_upstream.23.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.56
; user 0.56
; system 0.07
; cuser 0.45
; csystem 0.04