RegulonDB
RstA matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/RstA/RstA.EcolK12_2nt_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 /RstA.EcolK12_2nt_upstream.20.meme_quality_logo
; Input files
; input /RstA.EcolK12_2nt_upstream.20.meme_quality_matrix.tf
; prior /RstA.EcolK12_2nt_upstream.20.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /RstA.EcolK12_2nt_upstream.20.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 4 2 0 2 0 0 0 4 4 0 0 4 3 4 1 0 1 3 2 2
C 0 0 2 0 0 0 0 0 0 4 1 0 0 0 0 0 0 1 1 2
G 0 1 1 1 0 4 0 0 0 0 1 0 0 0 0 4 0 0 1 0
T 0 1 1 1 4 0 4 0 0 0 2 0 1 0 3 0 3 0 0 0
//
A 0.9 0.5 0.1 0.5 0.1 0.1 0.1 0.9 0.9 0.1 0.1 0.9 0.7 0.9 0.3 0.1 0.3 0.7 0.5 0.5
C 0.0 0.0 0.4 0.0 0.0 0.0 0.0 0.0 0.0 0.8 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.2 0.4
G 0.0 0.2 0.2 0.2 0.0 0.8 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.0 0.8 0.0 0.0 0.2 0.0
T 0.1 0.3 0.3 0.3 0.9 0.1 0.9 0.1 0.1 0.1 0.5 0.1 0.3 0.1 0.7 0.1 0.7 0.1 0.1 0.1
//
A 1.1 0.5 -1.6 0.5 -1.6 -1.6 -1.6 1.1 1.1 -1.6 -1.6 1.1 0.8 1.1 -0.1 -1.6 -0.1 0.8 0.5 0.5
C -1.6 -1.6 0.8 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 1.4 0.2 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 0.2 0.2 0.8
G -1.6 0.2 0.2 0.2 -1.6 1.4 -1.6 -1.6 -1.6 -1.6 0.2 -1.6 -1.6 -1.6 -1.6 1.4 -1.6 -1.6 0.2 -1.6
T -1.6 -0.1 -0.1 -0.1 1.1 -1.6 1.1 -1.6 -1.6 -1.6 0.4 -1.6 -0.1 -1.6 0.8 -1.6 0.8 -1.6 -1.6 -1.6
//
A 0.9 0.2 -0.1 0.2 -0.1 -0.1 -0.1 0.9 0.9 -0.1 -0.1 0.9 0.5 0.9 -0.0 -0.1 -0.0 0.5 0.2 0.2
C -0.1 -0.1 0.3 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 1.2 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.0 0.0 0.3
G -0.1 0.0 0.0 0.0 -0.1 1.2 -0.1 -0.1 -0.1 -0.1 0.0 -0.1 -0.1 -0.1 -0.1 1.2 -0.1 -0.1 0.0 -0.1
T -0.1 -0.0 -0.0 -0.0 0.9 -0.1 0.9 -0.1 -0.1 -0.1 0.2 -0.1 -0.0 -0.1 0.5 -0.1 0.5 -0.1 -0.1 -0.1
//
; Sites 4
>site_0
AACATGTAACTAAATGTAAC
>site_1
AGCGTGTAACGATATGTACA
>site_2
AATATGTAACCAAAAGTAAA
>site_3
ATGTTGTAACTAAATGACGC
;
; Matrix parameters
; Number of sites 4
; Columns 20
; 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 ADBDTGTAACBAAATGTAVM
; AC ADBDTGTAACBAAATGTAVM
; id ADBDTGTAACBAAATGTAVM
; name ADBDTGTAACBAAATGTAVM
; description ArsrTGTAACbAaAtGtmvm
; statistical_basis 4 sequences
; sites 4
; nb_sites 4
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 10.4547
; information.per.column 0.522733
; max.possible.info.per.col 1.58952
; consensus.strict AacaTGTAACtAaAtGtaac
; consensus.strict.rc GTTACATTTAGTTACATGTT
; consensus.IUPAC ArsrTGTAACbAaAtGtmvm
; consensus.IUPAC.rc KBKACATTTVGTTACAYSYT
; consensus.regexp A[ag][cg][ag]TGTAAC[cgt]AaAtGt[ac][acg][ac]
; consensus.regexp.rc [GT][CGT][GT]ACATTT[ACG]GTTACA[CT][CG][CT]T
; residues.content.crude.freq a:0.4500|c:0.1375|g:0.1625|t:0.2500
; G+C.content.crude.freq 0.3
; residues.content.corrected.freq a:0.4182|c:0.1516|g:0.1708|t:0.2594
; G+C.content.corrected.freq 0.322367
; min(P(S|M)) 5.22557e-28
; max(P(S|M)) 0.000344715
; proba_range 0.000344715
; Wmin -32.2
; Wmax 18.3
; Wrange 50.5
; logo file:/RstA.EcolK12_2nt_upstream.20.meme_quality_logo_m1.png
; logo file:/RstA.EcolK12_2nt_upstream.20.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161100
; Seconds 0.63
; user 0.63
; system 0.05
; cuser 0.43
; csystem 0.04