RegulonDB
UxuR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/UxuR/UxuR.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 /UxuR.EcolK12_1nt_upstream.21.meme_quality_logo
; Input files
; input /UxuR.EcolK12_1nt_upstream.21.meme_quality_matrix.tf
; prior /UxuR.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 /UxuR.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 5 0 0 1 0 0 0 7 8 0 0 7 5 4 0 2 0 2 1 2 2
C 1 3 1 0 0 0 4 0 0 5 8 0 1 0 1 1 1 1 1 0 3
G 0 3 0 7 7 0 0 1 0 0 0 0 1 0 1 0 3 3 2 6 0
T 2 2 7 0 1 8 4 0 0 3 0 1 1 4 6 5 4 2 4 0 3
//
A 0.6 0.0 0.0 0.1 0.0 0.0 0.0 0.8 0.9 0.0 0.0 0.8 0.6 0.5 0.0 0.3 0.0 0.3 0.1 0.3 0.3
C 0.1 0.4 0.1 0.0 0.0 0.0 0.5 0.0 0.0 0.6 0.9 0.0 0.1 0.0 0.1 0.1 0.1 0.1 0.1 0.0 0.4
G 0.0 0.4 0.0 0.8 0.8 0.0 0.0 0.1 0.0 0.0 0.0 0.0 0.1 0.0 0.1 0.0 0.4 0.4 0.2 0.7 0.0
T 0.3 0.3 0.8 0.0 0.1 0.9 0.5 0.0 0.0 0.4 0.0 0.1 0.1 0.5 0.7 0.6 0.5 0.3 0.5 0.0 0.4
//
A 0.7 -2.2 -2.2 -0.7 -2.2 -2.2 -2.2 1.0 1.2 -2.2 -2.2 1.0 0.7 0.5 -2.2 -0.1 -2.2 -0.1 -0.7 -0.1 -0.1
C -0.4 0.5 -0.4 -2.2 -2.2 -2.2 0.8 -2.2 -2.2 1.0 1.5 -2.2 -0.4 -2.2 -0.4 -0.4 -0.4 -0.4 -0.4 -2.2 0.5
G -2.2 0.6 -2.2 1.4 1.4 -2.2 -2.2 -0.4 -2.2 -2.2 -2.2 -2.2 -0.4 -2.2 -0.4 -2.2 0.6 0.6 0.2 1.2 -2.2
T -0.2 -0.2 1.0 -2.2 -0.7 1.1 0.5 -2.2 -2.2 0.2 -2.2 -0.7 -0.7 0.5 0.9 0.7 0.5 -0.2 0.5 -2.2 0.2
//
A 0.4 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.8 1.1 -0.1 -0.1 0.8 0.4 0.2 -0.1 -0.0 -0.1 -0.0 -0.1 -0.0 -0.0
C -0.1 0.2 -0.1 -0.1 -0.1 -0.1 0.4 -0.1 -0.1 0.6 1.3 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.2
G -0.0 0.2 -0.0 1.1 1.1 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.1 -0.0 0.2 0.2 0.0 0.8 -0.0
T -0.0 -0.0 0.8 -0.1 -0.1 1.0 0.2 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 0.2 0.6 0.4 0.2 -0.0 0.2 -0.1 0.1
//
; Sites 8
>site_0
ACTGGTCAACCAAATATCAGT
>site_1
TGCGGTTAATCAAATTTTTGC
>site_2
ACTGGTCAATCAAACTGATAT
>site_3
CCTGGTTAATCACATTGTGGC
>site_4
ATTAGTTAACCAATTCTGTGT
>site_5
TGTGGTTAACCAATTTCAGAA
>site_6
ATTGGTCAACCATTGTTGCGA
>site_7
AGTGTTCGACCTGTTAGGTGC
;
; Matrix parameters
; Number of sites 8
; 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 ABTGGTYAAYCAAWTTKDKGH
; AC ABTGGTYAAYCAAWTTKDKGH
; id ABTGGTYAAYCAAWTTKDKGH
; name ABTGGTYAAYCAAWTTKDKGH
; description asTGGTyAAYCAawttkgkGy
; statistical_basis 8 sequences
; sites 8
; nb_sites 8
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 10.7084
; information.per.column 0.509924
; max.possible.info.per.col 1.58873
; consensus.strict agTGGTcAACCAaattggtGc
; consensus.strict.rc GCACCAATTTGGTTGACCACT
; consensus.IUPAC asTGGTyAAYCAawttkgkGy
; consensus.IUPAC.rc RCMCMAAWTTGRTTRACCAST
; consensus.regexp a[cg]TGGT[ct]AA[CT]CAa[at]tt[gt]g[gt]G[ct]
; consensus.regexp.rc [AG]C[AC]C[AC]AA[AT]TTG[AG]TT[AG]ACCA[CG]T
; residues.content.crude.freq a:0.2738|c:0.1845|g:0.2024|t:0.3393
; G+C.content.crude.freq 0.386905
; residues.content.corrected.freq a:0.2757|c:0.1871|g:0.2026|t:0.3346
; G+C.content.corrected.freq 0.389665
; min(P(S|M)) 1.88634e-32
; max(P(S|M)) 3.62247e-05
; proba_range 3.62247e-05
; Wmin -41.5
; Wmax 18.8
; Wrange 60.3
; logo file:/UxuR.EcolK12_1nt_upstream.21.meme_quality_logo_m1.png
; logo file:/UxuR.EcolK12_1nt_upstream.21.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161129
; Job done 2019-06-03.161129
; Seconds 0.43
; user 0.43
; system 0.05
; cuser 0.29
; csystem 0.05