RegulonDB
ExuR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/ExuR/ExuR.EcolK12_1nt_upstream.20.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 /ExuR.EcolK12_1nt_upstream.20.meme_quality_logo
; Input files
; input /ExuR.EcolK12_1nt_upstream.20.meme_quality_matrix.tf
; prior /ExuR.EcolK12_1nt_upstream.20.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /ExuR.EcolK12_1nt_upstream.20.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 9 10 9 1 1 1 1 0 4 6 9 6 1 9 6 7 0 2 4 2
C 0 1 2 3 0 0 0 0 3 0 1 3 10 1 5 0 1 2 1 7
G 1 0 0 6 0 8 10 0 0 3 1 0 0 0 0 2 1 0 3 0
T 1 0 0 1 10 2 0 11 4 2 0 2 0 1 0 2 9 7 3 2
//
A 0.8 0.9 0.8 0.1 0.1 0.1 0.1 0.0 0.4 0.5 0.8 0.5 0.1 0.8 0.5 0.6 0.0 0.2 0.4 0.2
C 0.0 0.1 0.2 0.3 0.0 0.0 0.0 0.0 0.3 0.0 0.1 0.3 0.9 0.1 0.4 0.0 0.1 0.2 0.1 0.6
G 0.1 0.0 0.0 0.5 0.0 0.7 0.9 0.0 0.0 0.3 0.1 0.0 0.0 0.0 0.0 0.2 0.1 0.0 0.3 0.0
T 0.1 0.0 0.0 0.1 0.9 0.2 0.0 0.9 0.4 0.2 0.0 0.2 0.0 0.1 0.0 0.2 0.8 0.6 0.3 0.2
//
A 1.0 1.1 1.0 -1.0 -1.0 -1.0 -1.0 -2.5 0.2 0.6 1.0 0.6 -1.0 1.0 0.6 0.7 -2.5 -0.4 0.2 -0.4
C -2.5 -0.7 -0.1 0.3 -2.5 -2.5 -2.5 -2.5 0.3 -2.5 -0.7 0.3 1.4 -0.7 0.7 -2.5 -0.7 -0.1 -0.7 1.1
G -0.7 -2.5 -2.5 0.9 -2.5 1.2 1.4 -2.5 -2.5 0.3 -0.7 -2.5 -2.5 -2.5 -2.5 -0.1 -0.7 -2.5 0.3 -2.5
T -1.0 -2.5 -2.5 -1.0 1.1 -0.4 -2.5 1.2 0.2 -0.4 -2.5 -0.4 -2.5 -1.0 -2.5 -0.4 1.0 0.7 -0.1 -0.4
//
A 0.8 0.9 0.8 -0.1 -0.1 -0.1 -0.1 -0.1 0.1 0.3 0.8 0.3 -0.1 0.8 0.3 0.4 -0.1 -0.1 0.1 -0.1
C -0.0 -0.1 -0.0 0.1 -0.0 -0.0 -0.0 -0.0 0.1 -0.0 -0.1 0.1 1.2 -0.1 0.3 -0.0 -0.1 -0.0 -0.1 0.6
G -0.1 -0.0 -0.0 0.5 -0.0 0.8 1.2 -0.0 -0.0 0.1 -0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 0.1 -0.0
T -0.1 -0.1 -0.1 -0.1 0.9 -0.1 -0.1 1.1 0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.7 0.4 -0.0 -0.1
//
; Sites 11
>site_0
AAAGTGGTAGAACACATTGC
>site_1
AAACTGGTCAACCAAATATC
>site_2
AAATTGGTTAACCACATCAC
>site_3
AAAGTGGTATAACAAATATA
>site_4
AAAGTGGTAAATCTCGCTGC
>site_5
GACCTGGTTAATCACATTGT
>site_6
ACAATGGTTGACCAATTTAC
>site_7
AACGTAGTTAAAAAAATTAC
>site_8
AAAGTTGTATGACAAGTTAT
>site_9
AAAGTTATCACACCAATTTC
>site_10
TAACAGGTCGAACACTGCCA
;
; Matrix parameters
; Number of sites 11
; Columns 20
; 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 AAASTGGTHRAMCAMATTDC
; AC AAASTGGTHRAMCAMATTDC
; id AAASTGGTHRAMCAMATTDC
; name AAASTGGTHRAMCAMATTDC
; description aAasTGGThramCamattrC
; statistical_basis 11 sequences
; sites 11
; nb_sites 11
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 10.3768
; information.per.column 0.518839
; max.possible.info.per.col 1.58873
; consensus.strict aAagTGGTcaaaCacattgC
; consensus.strict.rc GCAATGTGTTTGACCACTTT
; consensus.IUPAC aAasTGGThramCamattrC
; consensus.IUPAC.rc GYAATKTGKTYDACCASTTT
; consensus.regexp aAa[cg]TGGT[act][ag]a[ac]Ca[ac]att[ag]C
; consensus.regexp.rc G[CT]AAT[GT]TG[GT]T[CT][AGT]ACCA[CG]TTT
; residues.content.crude.freq a:0.4000|c:0.1818|g:0.1591|t:0.2591
; G+C.content.crude.freq 0.340909
; residues.content.corrected.freq a:0.3909|c:0.1840|g:0.1628|t:0.2623
; G+C.content.corrected.freq 0.346812
; min(P(S|M)) 3.4849e-34
; max(P(S|M)) 0.000201917
; proba_range 0.000201917
; Wmin -46.5
; Wmax 18.1
; Wrange 64.6
; logo file:/ExuR.EcolK12_1nt_upstream.20.meme_quality_logo_m1.png
; logo file:/ExuR.EcolK12_1nt_upstream.20.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.58
; user 0.58
; system 0.06
; cuser 0.44
; csystem 0.04