RegulonDB
GadW matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/GadW/GadW.EcolK12_1nt_upstream.21.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 /GadW.EcolK12_1nt_upstream.21.meme_quality_logo
; Input files
; input /GadW.EcolK12_1nt_upstream.21.meme_quality_matrix.tf
; prior /GadW.EcolK12_1nt_upstream.21.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /GadW.EcolK12_1nt_upstream.21.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 6 11 3 9 2 8 14 15 6 15 3 5 14 3 8 2 10 1 2 7
C 1 2 1 3 0 2 4 1 2 3 1 2 8 2 0 3 12 3 0 0 3
G 1 3 1 1 5 2 1 1 0 1 0 1 0 0 10 4 0 1 1 4 1
T 12 6 4 10 3 11 4 1 0 7 1 11 4 1 4 2 3 3 15 11 6
//
A 0.2 0.3 0.6 0.2 0.5 0.1 0.5 0.8 0.8 0.3 0.8 0.2 0.3 0.8 0.2 0.5 0.1 0.6 0.1 0.1 0.4
C 0.1 0.1 0.1 0.2 0.0 0.1 0.2 0.1 0.1 0.2 0.1 0.1 0.5 0.1 0.0 0.2 0.7 0.2 0.0 0.0 0.2
G 0.1 0.2 0.1 0.1 0.3 0.1 0.1 0.1 0.0 0.1 0.0 0.1 0.0 0.0 0.6 0.2 0.0 0.1 0.1 0.2 0.1
T 0.7 0.3 0.2 0.6 0.2 0.6 0.2 0.1 0.0 0.4 0.1 0.6 0.2 0.1 0.2 0.1 0.2 0.2 0.8 0.6 0.3
//
A -0.5 0.2 0.8 -0.5 0.6 -0.8 0.5 1.0 1.1 0.2 1.1 -0.5 0.0 1.0 -0.5 0.5 -0.8 0.7 -1.4 -0.8 0.3
C -1.1 -0.5 -1.1 -0.2 -2.9 -0.5 0.1 -1.1 -0.5 -0.2 -1.1 -0.5 0.8 -0.5 -2.9 -0.2 1.2 -0.2 -2.9 -2.9 -0.2
G -1.1 -0.1 -1.1 -1.1 0.3 -0.5 -1.1 -1.1 -2.9 -1.1 -2.9 -1.1 -2.9 -2.9 1.0 0.1 -2.9 -1.1 -1.1 0.1 -1.1
T 0.8 0.2 -0.2 0.7 -0.5 0.7 -0.2 -1.4 -2.9 0.3 -1.4 0.7 -0.2 -1.4 -0.2 -0.8 -0.5 -0.5 1.1 0.7 0.2
//
A -0.1 0.1 0.5 -0.1 0.3 -0.1 0.2 0.8 0.9 0.1 0.9 -0.1 0.0 0.8 -0.1 0.2 -0.1 0.4 -0.1 -0.1 0.1
C -0.1 -0.1 -0.1 -0.0 -0.0 -0.1 0.0 -0.1 -0.1 -0.0 -0.1 -0.1 0.4 -0.1 -0.0 -0.0 0.8 -0.0 -0.0 -0.0 -0.0
G -0.1 -0.0 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0 -0.1 -0.0 -0.0 0.6 0.0 -0.0 -0.1 -0.1 0.0 -0.1
T 0.6 0.1 -0.1 0.4 -0.1 0.5 -0.1 -0.1 -0.0 0.1 -0.1 0.5 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.9 0.5 0.1
//
; Sites 17
>site_0
TCACGTAAAAATCAGACCTTA
>site_1
TAATATTAAAAACAGACTTTA
>site_2
AAATATCAAAATCAGATATTT
>site_3
TTACGTTACTATCAGGCATAT
>site_4
GGATATAAACATCAGACAGGT
>site_5
TAATATAAACATTTAACATGA
>site_6
TTTTATAAACATAAGCTATAC
>site_7
TACGGAAAATATCAGCCATGA
>site_8
TGGAAATAAGATCAGCCATTT
>site_9
TTATTTCAATACAATGAGTTA
>site_10
TCATTGAAAAACAATACAATA
>site_11
TGTTATTTAAATTAAGCCTGT
>site_12
AAATATCACTATTAGTACTTG
>site_13
AATTAGCCATTTCAAACATTA
>site_14
TTTATTAAATCGACTGCATTC
>site_15
CTAAGCAGAAAAACGACTTTT
>site_16
TTACGCGAATAATATTTTTTC
;
; Matrix parameters
; Number of sites 17
; Columns 21
; 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 TDATRTHAAWATHAGRCATTW
; AC TDATRTHAAWATHAGRCATTW
; id TDATRTHAAWATHAGRCATTW
; name TDATRTHAAWATHAGRCATTW
; description twatrtmAAwAtmAGrCaTkw
; statistical_basis 17 sequences
; sites 17
; nb_sites 17
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 7.09478
; information.per.column 0.337847
; max.possible.info.per.col 1.58873
; consensus.strict taatataAAtAtcAGaCaTta
; consensus.strict.rc TAATGTCTGATATTTATATTA
; consensus.IUPAC twatrtmAAwAtmAGrCaTkw
; consensus.IUPAC.rc WMATGYCTKATWTTKAYATWA
; consensus.regexp t[at]at[ag]t[ac]AA[at]At[ac]AG[ag]CaT[gt][at]
; consensus.regexp.rc [AT][AC]ATG[CT]CT[GT]AT[AT]TT[GT]A[CT]AT[AT]A
; residues.content.crude.freq a:0.4118|c:0.1485|g:0.1064|t:0.3333
; G+C.content.crude.freq 0.254902
; residues.content.corrected.freq a:0.4051|c:0.1517|g:0.1119|t:0.3313
; G+C.content.corrected.freq 0.263615
; min(P(S|M)) 1.70843e-31
; max(P(S|M)) 1.47747e-05
; proba_range 1.47747e-05
; Wmin -38.6
; Wmax 15.7
; Wrange 54.3
; logo file:/GadW.EcolK12_1nt_upstream.21.meme_quality_logo_m1.png
; logo file:/GadW.EcolK12_1nt_upstream.21.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160930
; Seconds 0.59
; user 0.59
; system 0.06
; cuser 0.46
; csystem 0.05