RegulonDB
YdeO matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/YdeO/YdeO.EcolK12_2nt_upstream.31.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 /YdeO.EcolK12_2nt_upstream.31.meme_quality_logo
; Input files
; input /YdeO.EcolK12_2nt_upstream.31.meme_quality_matrix.tf
; prior /YdeO.EcolK12_2nt_upstream.31.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /YdeO.EcolK12_2nt_upstream.31.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 1 1 1 0 5 1 0 0 1 1 5 1 0 5 0 2 3 3 3 6 0 1 2 3 4 3 2 2 1 2 0
C 0 0 2 3 0 0 0 1 2 3 1 1 2 0 1 0 3 0 1 0 0 0 0 2 0 0 0 2 2 2 5
G 2 2 1 1 0 1 0 0 0 0 0 2 3 1 0 1 0 0 2 0 3 5 2 1 1 1 1 0 1 1 0
T 3 3 2 2 1 4 6 5 3 2 0 2 1 0 5 3 0 3 0 0 3 0 2 0 1 2 3 2 2 1 1
//
A 0.2 0.2 0.2 0.0 0.8 0.2 0.0 0.0 0.2 0.2 0.8 0.2 0.0 0.8 0.0 0.3 0.5 0.5 0.5 0.9 0.0 0.2 0.3 0.5 0.6 0.5 0.3 0.3 0.2 0.3 0.0
C 0.0 0.0 0.3 0.5 0.0 0.0 0.0 0.2 0.3 0.5 0.2 0.2 0.3 0.0 0.2 0.0 0.5 0.0 0.2 0.0 0.0 0.0 0.0 0.3 0.0 0.0 0.0 0.3 0.3 0.3 0.7
G 0.3 0.3 0.2 0.2 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.3 0.5 0.2 0.0 0.2 0.0 0.0 0.3 0.0 0.5 0.7 0.3 0.2 0.2 0.2 0.2 0.0 0.2 0.2 0.0
T 0.5 0.5 0.3 0.3 0.2 0.6 0.9 0.8 0.5 0.3 0.0 0.3 0.2 0.0 0.8 0.5 0.0 0.5 0.0 0.0 0.5 0.0 0.3 0.0 0.2 0.3 0.5 0.3 0.3 0.2 0.2
//
A -0.5 -0.5 -0.5 -1.9 1.0 -0.5 -1.9 -1.9 -0.5 -0.5 1.0 -0.5 -1.9 1.0 -1.9 0.1 0.5 0.5 0.5 1.1 -1.9 -0.5 0.1 0.5 0.7 0.5 0.1 0.1 -0.5 0.1 -1.9
C -1.9 -1.9 0.4 0.8 -1.9 -1.9 -1.9 -0.2 0.4 0.8 -0.2 -0.2 0.4 -1.9 -0.2 -1.9 0.8 -1.9 -0.2 -1.9 -1.9 -1.9 -1.9 0.4 -1.9 -1.9 -1.9 0.4 0.4 0.4 1.3
G 0.4 0.4 -0.2 -0.2 -1.9 -0.2 -1.9 -1.9 -1.9 -1.9 -1.9 0.4 0.8 -0.2 -1.9 -0.2 -1.9 -1.9 0.4 -1.9 0.8 1.3 0.4 -0.2 -0.2 -0.2 -0.2 -1.9 -0.2 -0.2 -1.9
T 0.5 0.5 0.1 0.1 -0.5 0.7 1.1 0.9 0.5 0.1 -1.9 0.1 -0.5 -1.9 0.9 0.5 -1.9 0.5 -1.9 -1.9 0.5 -1.9 0.1 -1.9 -0.5 0.1 0.5 0.1 0.1 -0.5 -0.5
//
A -0.1 -0.1 -0.1 -0.1 0.7 -0.1 -0.1 -0.1 -0.1 -0.1 0.7 -0.1 -0.1 0.7 -0.1 0.0 0.2 0.2 0.2 1.0 -0.1 -0.1 0.0 0.2 0.5 0.2 0.0 0.0 -0.1 0.0 -0.1
C -0.1 -0.1 0.1 0.4 -0.1 -0.1 -0.1 -0.0 0.1 0.4 -0.0 -0.0 0.1 -0.1 -0.0 -0.1 0.4 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 0.1 0.1 0.1 0.9
G 0.1 0.1 -0.0 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 0.1 0.4 -0.0 -0.1 -0.0 -0.1 -0.1 0.1 -0.1 0.4 1.0 0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.1
T 0.2 0.2 0.0 0.0 -0.1 0.4 1.0 0.7 0.2 0.0 -0.1 0.0 -0.1 -0.1 0.7 0.2 -0.1 0.2 -0.1 -0.1 0.2 -0.1 0.0 -0.1 -0.1 0.0 0.2 0.0 0.0 -0.1 -0.1
//
; Sites 6
>site_0
TGTTATTTCCACGATGCAAATGACAATACCC
>site_1
GTAGAGTTTCAGGATAAAGAGGGAGATCTAC
>site_2
TTTCAATTTCAGTATACTAATGAAATGATGC
>site_3
GTCCATTTTTATCGCTAAAAGATAAATCCAC
>site_4
TAGTTTTCATCTGATTCTGAGGTGATATGCC
>site_5
AGCCATTTCAAACATTATCATGGCTGATATT
;
; Matrix parameters
; Number of sites 6
; Columns 31
; 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 KKNYATTTYYANSATWMWRAKGDMAWWHNNC
; AC KKNYATTTYYANSATWMWRAKGDMAWWHNNC
; id KKNYATTTYYANSATWMWRAKGDMAWWHNNC
; name KKNYATTTYYANSATWMWRAKGDMAWWHNNC
; description kkyyatTtyyaksatwmwrAkGdmawwhymC
; statistical_basis 6 sequences
; sites 6
; nb_sites 6
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 10.562
; information.per.column 0.340709
; max.possible.info.per.col 1.58952
; consensus.strict ttccatTttcaggattcaaAgGgaaatcccC
; consensus.strict.rc GGGGATTTCCCTTTGAATCCTGAAAATGGAA
; consensus.IUPAC kkyyatTtyyaksatwmwrAkGdmawwhymC
; consensus.IUPAC.rc GKRDWWTKHCMTYWKWATSMTRRAAATRRMM
; consensus.regexp [gt][gt][ct][ct]atTt[ct][ct]a[gt][cg]at[at][ac][at][ag]A[gt]G[agt][ac]a[at][at][act][ct][ac]C
; consensus.regexp.rc G[GT][AG][AGT][AT][AT]T[GT][ACT]C[AC]T[CT][AT][GT][AT]AT[CG][AC]T[AG][AG]AAAT[AG][AG][AC][AC]
; residues.content.crude.freq a:0.3172|c:0.1774|g:0.1720|t:0.3333
; G+C.content.crude.freq 0.349462
; residues.content.corrected.freq a:0.3135|c:0.1818|g:0.1766|t:0.3281
; G+C.content.corrected.freq 0.358373
; min(P(S|M)) 1.62248e-44
; max(P(S|M)) 1.25171e-09
; proba_range 1.25171e-09
; Wmin -54.4
; Wmax 21.8
; Wrange 76.2
; logo file:/YdeO.EcolK12_2nt_upstream.31.meme_quality_logo_m1.png
; logo file:/YdeO.EcolK12_2nt_upstream.31.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161129
; Job done 2019-06-03.161129
; Seconds 0.56
; user 0.56
; system 0.05
; cuser 0.45
; csystem 0.05