RegulonDB
AcrR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/AcrR/AcrR.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 /AcrR.EcolK12_2nt_upstream.14.meme_quality_logo
; Input files
; input /AcrR.EcolK12_2nt_upstream.14.meme_quality_matrix.tf
; prior /AcrR.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 /AcrR.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 0 3 1 4 0 2 1 5 1 0 0 0 3 0
C 2 0 4 0 0 0 4 0 1 1 0 1 0 1
G 1 0 0 1 0 0 0 0 0 0 1 4 0 4
T 2 2 0 0 5 3 0 0 3 4 4 0 2 0
//
A 0.0 0.5 0.2 0.7 0.0 0.4 0.2 0.9 0.2 0.0 0.0 0.0 0.5 0.0
C 0.4 0.0 0.7 0.0 0.0 0.0 0.7 0.0 0.2 0.2 0.0 0.2 0.0 0.2
G 0.2 0.0 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.7 0.0 0.7
T 0.4 0.4 0.0 0.0 0.9 0.5 0.0 0.0 0.5 0.7 0.7 0.0 0.4 0.0
//
A -1.8 0.6 -0.3 0.9 -1.8 0.3 -0.3 1.1 -0.3 -1.8 -1.8 -1.8 0.6 -1.8
C 0.6 -1.8 1.2 -1.8 -1.8 -1.8 1.2 -1.8 -0.0 -0.0 -1.8 -0.0 -1.8 -0.0
G -0.0 -1.8 -1.8 -0.0 -1.8 -1.8 -1.8 -1.8 -1.8 -1.8 -0.0 1.2 -1.8 1.2
T 0.3 0.3 -1.8 -1.8 1.1 0.6 -1.8 -1.8 0.6 0.9 0.9 -1.8 0.3 -1.8
//
A -0.1 0.3 -0.1 0.6 -0.1 0.1 -0.1 1.0 -0.1 -0.1 -0.1 -0.1 0.3 -0.1
C 0.2 -0.1 0.9 -0.1 -0.1 -0.1 0.9 -0.1 -0.0 -0.0 -0.1 -0.0 -0.1 -0.0
G -0.0 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 0.9 -0.1 0.9
T 0.1 0.1 -0.1 -0.1 1.0 0.3 -0.1 -0.1 0.3 0.6 0.6 -0.1 0.1 -0.1
//
; Sites 5
>site_0
TACATACATTTGTG
>site_1
TTCATTCATTTGAC
>site_2
GTCATTCATTTCTG
>site_3
CACATACAACGGAG
>site_4
CAAGTTAACTTGAG
;
; Matrix parameters
; Number of sites 5
; 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 BWCATWCATTTGWG
; AC BWCATWCATTTGWG
; id BWCATWCATTTGWG
; name BWCATWCATTTGWG
; description ywCaTwCAtttGwG
; statistical_basis 5 sequences
; sites 5
; nb_sites 5
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 6.98633
; information.per.column 0.499023
; max.possible.info.per.col 1.58952
; consensus.strict caCaTtCAtttGaG
; consensus.strict.rc CTCAAATGAATGTG
; consensus.IUPAC ywCaTwCAtttGwG
; consensus.IUPAC.rc CWCAAATGWATGWR
; consensus.regexp [ct][at]CaT[at]CAtttG[at]G
; consensus.regexp.rc C[AT]CAAATG[AT]ATG[AT][AG]
; residues.content.crude.freq a:0.2857|c:0.2000|g:0.1571|t:0.3571
; G+C.content.crude.freq 0.357143
; residues.content.corrected.freq a:0.2866|c:0.2013|g:0.1650|t:0.3471
; G+C.content.corrected.freq 0.366258
; min(P(S|M)) 8.33059e-21
; max(P(S|M)) 0.00239837
; proba_range 0.00239837
; Wmin -25.1
; Wmax 12.9
; Wrange 38
; logo file:/AcrR.EcolK12_2nt_upstream.14.meme_quality_logo_m1.png
; logo file:/AcrR.EcolK12_2nt_upstream.14.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160930
; Seconds 0.56
; user 0.56
; system 0.06
; cuser 0.42
; csystem 0.05