RegulonDB
NhaR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/NhaR/NhaR.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 /NhaR.EcolK12_1nt_upstream.21.meme_quality_logo
; Input files
; input /NhaR.EcolK12_1nt_upstream.21.meme_quality_matrix.tf
; prior /NhaR.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 /NhaR.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 1 2 2 2 2 0 2 1 4 6 3 5 3 3 0 0 3 4 1 0 3
C 0 2 2 1 0 5 0 1 0 0 0 0 0 2 6 0 0 1 1 0 1
G 0 1 1 0 0 0 4 3 0 0 0 0 0 0 0 3 3 0 0 0 0
T 5 1 1 3 4 1 0 1 2 0 3 1 3 1 0 3 0 1 4 6 2
//
A 0.2 0.3 0.3 0.3 0.3 0.0 0.3 0.2 0.6 0.9 0.5 0.8 0.5 0.5 0.0 0.0 0.5 0.6 0.2 0.0 0.5
C 0.0 0.3 0.3 0.2 0.0 0.7 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.3 0.9 0.0 0.0 0.2 0.2 0.0 0.2
G 0.0 0.2 0.2 0.0 0.0 0.0 0.6 0.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 0.5 0.0 0.0 0.0 0.0
T 0.8 0.2 0.2 0.5 0.6 0.2 0.0 0.2 0.3 0.0 0.5 0.2 0.5 0.2 0.0 0.5 0.0 0.2 0.6 0.9 0.3
//
A -0.5 0.1 0.1 0.1 0.1 -1.9 0.1 -0.5 0.7 1.1 0.5 1.0 0.5 0.5 -1.9 -1.9 0.5 0.7 -0.5 -1.9 0.5
C -1.9 0.4 0.4 -0.2 -1.9 1.3 -1.9 -0.2 -1.9 -1.9 -1.9 -1.9 -1.9 0.4 1.5 -1.9 -1.9 -0.2 -0.2 -1.9 -0.2
G -1.9 -0.2 -0.2 -1.9 -1.9 -1.9 1.1 0.8 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 0.8 0.8 -1.9 -1.9 -1.9 -1.9
T 0.9 -0.5 -0.5 0.5 0.7 -0.5 -1.9 -0.5 0.1 -1.9 0.5 -0.5 0.5 -0.5 -1.9 0.5 -1.9 -0.5 0.7 1.1 0.1
//
A -0.1 0.0 0.0 0.0 0.0 -0.1 0.0 -0.1 0.5 1.0 0.2 0.7 0.2 0.2 -0.1 -0.1 0.2 0.5 -0.1 -0.1 0.2
C -0.1 0.1 0.1 -0.0 -0.1 0.9 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 0.1 1.3 -0.1 -0.1 -0.0 -0.0 -0.1 -0.0
G -0.1 -0.0 -0.0 -0.1 -0.1 -0.1 0.6 0.4 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.4 0.4 -0.1 -0.1 -0.1 -0.1
T 0.7 -0.1 -0.1 0.2 0.4 -0.1 -0.1 -0.1 0.0 -0.1 0.2 -0.1 0.2 -0.1 -0.1 0.2 -0.1 -0.1 0.4 1.0 0.0
//
; Sites 6
>site_0
TTATTCGGAATATCCTGCTTA
>site_1
TGCATCGGAATTTACTGATTT
>site_2
TAGCTCGTAAAAAACGAATTA
>site_3
TCCTACACTATAATCTGATTT
>site_4
ACTTTCGAAAAATCCGAAATC
>site_5
TAAAATAGTAAAAACGATCTA
;
; Matrix parameters
; Number of sites 6
; 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 TNNWWCRGWAWAWMCKRATTW
; AC TNNWWCRGWAWAWMCKRATTW
; id TNNWWCRGWAWAWMCKRATTW
; name TNNWWCRGWAWAWMCKRATTW
; description tmmwwCRgwAwawmCkratTw
; statistical_basis 6 sequences
; sites 6
; nb_sites 6
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 8.66034
; information.per.column 0.412397
; max.possible.info.per.col 1.58873
; consensus.strict tccttCGgaAaaaaCggatTa
; consensus.strict.rc TAATCCGTTTTTTCCGAAGGA
; consensus.IUPAC tmmwwCRgwAwawmCkratTw
; consensus.IUPAC.rc WAATYMGKWTWTWCYGWWKKA
; consensus.regexp t[ac][ac][at][at]C[AG]g[at]A[at]a[at][ac]C[gt][ag]atT[at]
; consensus.regexp.rc [AT]AAT[CT][AC]G[GT][AT]T[AT]T[AT]C[CT]G[AT][AT][GT][GT]A
; residues.content.crude.freq a:0.3730|c:0.1746|g:0.1190|t:0.3333
; G+C.content.crude.freq 0.293651
; residues.content.corrected.freq a:0.3613|c:0.1793|g:0.1312|t:0.3282
; G+C.content.corrected.freq 0.310521
; min(P(S|M)) 1.25321e-30
; max(P(S|M)) 6.5085e-06
; proba_range 6.5085e-06
; Wmin -36.5
; Wmax 16.6
; Wrange 53.1
; logo file:/NhaR.EcolK12_1nt_upstream.21.meme_quality_logo_m1.png
; logo file:/NhaR.EcolK12_1nt_upstream.21.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161044
; Job done 2019-06-03.161045
; Seconds 0.56
; user 0.56
; system 0.06
; cuser 0.42
; csystem 0.05