RegulonDB
RcdA matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/RcdA/RcdA.EcolK12_2nt_upstream.14.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 /RcdA.EcolK12_2nt_upstream.14.meme_quality_logo
; Input files
; input /RcdA.EcolK12_2nt_upstream.14.meme_quality_matrix.tf
; prior /RcdA.EcolK12_2nt_upstream.14.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /RcdA.EcolK12_2nt_upstream.14.meme_quality_matrix_info.txt
; Output format tab
; pseudo-weight 1
; Background model
; Strand undef
; Background pseudo-frequency 0.01
; Residue probabilities
; a 0.29114
; c 0.20781
; g 0.20402
; t 0.29702
A 6 2 0 1 2 0 7 2 8 2 3 4 0 0
C 0 0 1 1 0 4 0 5 0 3 1 4 1 1
G 0 0 7 1 5 0 1 0 0 2 3 0 0 7
T 2 6 0 5 1 4 0 1 0 1 1 0 7 0
//
A 0.7 0.3 0.0 0.1 0.3 0.0 0.8 0.3 0.9 0.3 0.4 0.5 0.0 0.0
C 0.0 0.0 0.1 0.1 0.0 0.5 0.0 0.6 0.0 0.4 0.1 0.5 0.1 0.1
G 0.0 0.0 0.8 0.1 0.6 0.0 0.1 0.0 0.0 0.2 0.4 0.0 0.0 0.8
T 0.3 0.7 0.0 0.6 0.1 0.5 0.0 0.1 0.0 0.1 0.1 0.0 0.8 0.0
//
A 0.9 -0.1 -2.2 -0.7 -0.1 -2.2 1.0 -0.1 1.2 -0.1 0.2 0.5 -2.2 -2.2
C -2.2 -2.2 -0.4 -0.4 -2.2 0.8 -2.2 1.0 -2.2 0.5 -0.4 0.8 -0.4 -0.4
G -2.2 -2.2 1.4 -0.4 1.0 -2.2 -0.4 -2.2 -2.2 0.2 0.6 -2.2 -2.2 1.4
T -0.2 0.9 -2.2 0.7 -0.7 0.5 -2.2 -0.7 -2.2 -0.7 -0.7 -2.2 1.0 -2.2
//
A 0.6 -0.0 -0.1 -0.1 -0.0 -0.1 0.8 -0.0 1.1 -0.0 0.1 0.2 -0.1 -0.1
C -0.1 -0.1 -0.1 -0.1 -0.1 0.4 -0.1 0.6 -0.1 0.2 -0.1 0.4 -0.1 -0.1
G -0.0 -0.0 1.1 -0.1 0.6 -0.0 -0.1 -0.0 -0.0 0.0 0.2 -0.0 -0.0 1.1
T -0.0 0.6 -0.1 0.4 -0.1 0.2 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.8 -0.1
//
; Sites 8
>site_0
ATGTGTACAGAATG
>site_1
ATGTACAAACGCTG
>site_2
ATGTGCATAGCCTG
>site_3
AAGAGTACACAATG
>site_4
TTGCGCACAAGCCG
>site_5
ATCGTTACACGCTG
>site_6
AAGTGTACATAATC
>site_7
TTGTACGAAATATG
;
; Matrix parameters
; Number of sites 8
; Columns 14
; Rows 4
; Alphabet A|C|G|T
; Prior A:0.291144263562772|C:0.207810681831126|G:0.204024081631615|T:0.297020972974487|a:0.291144263562772|c:0.207810681831126|g:0.204024081631615|t:0.297020972974487
; program transfac
; matrix.nb 1
; accession ATGTGYACAVRMTG
; AC ATGTGYACAVRMTG
; id ATGTGYACAVRMTG
; name ATGTGYACAVRMTG
; description atGtGyACAsrmTG
; statistical_basis 8 sequences
; sites 8
; nb_sites 8
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 7.09102
; information.per.column 0.506501
; max.possible.info.per.col 1.58952
; consensus.strict atGtGcACAcgcTG
; consensus.strict.rc CAGCGTGTGCACAT
; consensus.IUPAC atGtGyACAsrmTG
; consensus.IUPAC.rc CAKYSTGTRCACAT
; consensus.regexp atGtG[ct]ACA[cg][ag][ac]TG
; consensus.regexp.rc CA[GT][CT][CG]TGT[AG]CACAT
; residues.content.crude.freq a:0.3304|c:0.1875|g:0.2321|t:0.2500
; G+C.content.crude.freq 0.419643
; residues.content.corrected.freq a:0.3260|c:0.1898|g:0.2290|t:0.2552
; G+C.content.corrected.freq 0.418775
; min(P(S|M)) 4.44128e-21
; max(P(S|M)) 0.00110789
; proba_range 0.00110789
; Wmin -26.4
; Wmax 13.2
; Wrange 39.6
; logo file:/RcdA.EcolK12_2nt_upstream.14.meme_quality_logo_m1.png
; logo file:/RcdA.EcolK12_2nt_upstream.14.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161100
; Seconds 0.57
; user 0.57
; system 0.04
; cuser 0.4
; csystem 0.04