RegulonDB
GntR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/GntR/GntR.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 /GntR.EcolK12_1nt_upstream.22.meme_quality_logo
; Input files
; input /GntR.EcolK12_1nt_upstream.22.meme_quality_matrix.tf
; prior /GntR.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 /GntR.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 5 2 0 1 2 8 1 0 0 1 0 7 7 1 9 2 4 4 1 3 9 5
C 2 3 0 0 1 0 5 5 6 0 1 1 0 7 0 0 1 1 3 3 0 0
G 0 0 9 1 0 0 0 2 2 7 0 0 0 0 0 1 0 1 3 1 0 0
T 2 4 0 7 6 1 3 2 1 1 8 1 2 1 0 6 4 3 2 2 0 4
//
A 0.5 0.2 0.0 0.1 0.2 0.8 0.1 0.0 0.0 0.1 0.0 0.7 0.7 0.1 0.9 0.2 0.4 0.4 0.1 0.3 0.9 0.5
C 0.2 0.3 0.0 0.0 0.1 0.0 0.5 0.5 0.6 0.0 0.1 0.1 0.0 0.7 0.0 0.0 0.1 0.1 0.3 0.3 0.0 0.0
G 0.0 0.0 0.9 0.1 0.0 0.0 0.0 0.2 0.2 0.7 0.0 0.0 0.0 0.0 0.0 0.1 0.0 0.1 0.3 0.1 0.0 0.0
T 0.2 0.4 0.0 0.7 0.6 0.1 0.3 0.2 0.1 0.1 0.8 0.1 0.2 0.1 0.0 0.6 0.4 0.3 0.2 0.2 0.0 0.4
//
A 0.6 -0.2 -2.3 -0.8 -0.2 1.0 -0.8 -2.3 -2.3 -0.8 -2.3 0.9 0.9 -0.8 1.2 -0.2 0.4 0.4 -0.8 0.1 1.2 0.6
C 0.1 0.4 -2.3 -2.3 -0.5 -2.3 0.9 0.9 1.1 -2.3 -0.5 -0.5 -2.3 1.2 -2.3 -2.3 -0.5 -0.5 0.4 0.4 -2.3 -2.3
G -2.3 -2.3 1.5 -0.5 -2.3 -2.3 -2.3 0.1 0.1 1.3 -2.3 -2.3 -2.3 -2.3 -2.3 -0.5 -2.3 -0.5 0.5 -0.5 -2.3 -2.3
T -0.3 0.4 -2.3 0.9 0.8 -0.8 0.1 -0.3 -0.8 -0.8 1.0 -0.8 -0.3 -0.8 -2.3 0.8 0.4 0.1 -0.3 -0.3 -2.3 0.4
//
A 0.3 -0.1 -0.1 -0.1 -0.1 0.9 -0.1 -0.1 -0.1 -0.1 -0.1 0.7 0.7 -0.1 1.1 -0.1 0.2 0.2 -0.1 0.0 1.1 0.3
C 0.0 0.1 -0.0 -0.0 -0.1 -0.0 0.5 0.5 0.7 -0.0 -0.1 -0.1 -0.0 0.9 -0.0 -0.0 -0.1 -0.1 0.1 0.1 -0.0 -0.0
G -0.0 -0.0 1.4 -0.1 -0.0 -0.0 -0.0 0.0 0.0 0.9 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.1 0.1 -0.1 -0.0 -0.0
T -0.1 0.2 -0.1 0.7 0.5 -0.1 0.0 -0.1 -0.1 -0.1 0.9 -0.1 -0.1 -0.1 -0.1 0.5 0.2 0.0 -0.1 -0.1 -0.1 0.2
//
; Sites 9
>site_0
CAGTTACCCGTAACATTTTTAA
>site_1
ATGTTACCGGTAAAATAACCAT
>site_2
ATGTTACCCGTATCATTCACAT
>site_3
ACGTTACCCATAACAAATGAAA
>site_4
ACGTTATGCGTAACATAGTAAT
>site_5
TTGTTACGCGTAACAAATCGAA
>site_6
TTGTAATTCTTATCAGTAGAAA
>site_7
CAGAAAATTGTTACATTACTAT
>site_8
ACGGCTTCGGCCATATCAGCAA
;
; Matrix parameters
; Number of sites 9
; 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 AHGTTAYCCGTAACATWWBHAW
; AC AHGTTAYCCGTAACATWWBHAW
; id AHGTTAYCCGTAACATWWBHAW
; name AHGTTAYCCGTAACATWWBHAW
; description myGttAysSGTaaCAtwwsmAw
; statistical_basis 9 sequences
; sites 9
; nb_sites 9
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 10.1886
; information.per.column 0.46312
; max.possible.info.per.col 1.58873
; consensus.strict acGttAccCGTaaCAtaagcAa
; consensus.strict.rc TTGCTTATGTTACGGGTAACGT
; consensus.IUPAC myGttAysSGTaaCAtwwsmAw
; consensus.IUPAC.rc WTKSWWATGTTACSSRTAACRK
; consensus.regexp [ac][ct]GttA[ct][cg][CG]GTaaCAt[at][at][cg][ac]A[at]
; consensus.regexp.rc [AT]T[GT][CG][AT][AT]ATGTTAC[CG][CG][AG]TAAC[AG][GT]
; residues.content.crude.freq a:0.3636|c:0.1970|g:0.1364|t:0.3030
; G+C.content.crude.freq 0.333333
; residues.content.corrected.freq a:0.3564|c:0.1980|g:0.1431|t:0.3025
; G+C.content.corrected.freq 0.341175
; min(P(S|M)) 3.15319e-35
; max(P(S|M)) 1.7209e-05
; proba_range 1.7209e-05
; Wmin -45.7
; Wmax 18.9
; Wrange 64.6
; logo file:/GntR.EcolK12_1nt_upstream.22.meme_quality_logo_m1.png
; logo file:/GntR.EcolK12_1nt_upstream.22.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.6
; user 0.6
; system 0.06
; cuser 0.43
; csystem 0.05