RegulonDB
NarP matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/NarP/NarP.EcolK12_2nt_upstream.16.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 /NarP.EcolK12_2nt_upstream.16.meme_quality_logo
; Input files
; input /NarP.EcolK12_2nt_upstream.16.meme_quality_matrix.tf
; prior /NarP.EcolK12_2nt_upstream.16.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /NarP.EcolK12_2nt_upstream.16.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 1 8 5 1 0 6 5 6 6 6 2 0 6 2 1 8
C 0 2 5 11 7 5 0 1 2 5 0 2 0 0 1 0
G 0 1 1 0 0 0 2 0 1 1 8 3 5 9 0 4
T 11 1 1 0 5 1 5 5 3 0 2 7 1 1 10 0
//
A 0.1 0.6 0.4 0.1 0.0 0.5 0.4 0.5 0.5 0.5 0.2 0.0 0.5 0.2 0.1 0.6
C 0.0 0.2 0.4 0.9 0.6 0.4 0.0 0.1 0.2 0.4 0.0 0.2 0.0 0.0 0.1 0.0
G 0.0 0.1 0.1 0.0 0.0 0.0 0.2 0.0 0.1 0.1 0.6 0.2 0.4 0.7 0.0 0.3
T 0.9 0.1 0.1 0.0 0.4 0.1 0.4 0.4 0.3 0.0 0.2 0.6 0.1 0.1 0.8 0.0
//
A -1.1 0.8 0.3 -1.1 -2.6 0.5 0.3 0.5 0.5 0.5 -0.5 -2.6 0.5 -0.5 -1.1 0.8
C -2.6 -0.2 0.7 1.4 1.0 0.7 -2.6 -0.8 -0.2 0.7 -2.6 -0.2 -2.6 -2.6 -0.8 -2.6
G -2.6 -0.8 -0.8 -2.6 -2.6 -2.6 -0.2 -2.6 -0.8 -0.8 1.1 0.2 0.7 1.2 -2.6 0.5
T 1.1 -1.1 -1.1 -2.6 0.3 -1.1 0.3 0.3 -0.2 -2.6 -0.5 0.6 -1.1 -1.1 1.0 -2.6
//
A -0.1 0.5 0.1 -0.1 -0.1 0.2 0.1 0.2 0.2 0.2 -0.1 -0.1 0.2 -0.1 -0.1 0.5
C -0.0 -0.0 0.3 1.2 0.5 0.3 -0.0 -0.1 -0.0 0.3 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0
G -0.0 -0.1 -0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1 -0.1 0.7 0.0 0.3 0.9 -0.0 0.1
T 0.9 -0.1 -0.1 -0.1 0.1 -0.1 0.1 0.1 -0.0 -0.1 -0.1 0.4 -0.1 -0.1 0.8 -0.1
//
; Sites 12
>site_0
TACCCATTAAGGAGTA
>site_1
TAACTCTAAAGTGGTA
>site_2
TACCCCGATCGGGGTA
>site_3
TACCTCAATAGCGGTA
>site_4
TAACCAATAAATGGTA
>site_5
TAACCCTTACGTAGCA
>site_6
TGCCCATTAATGAGTA
>site_7
TACCTCTCTGGCGGTA
>site_8
TCGCCAGAAAGTATTG
>site_9
TTAATAAAGCGTAGTG
>site_10
AAACTAATCCTTTATG
>site_11
TCTCCTAACCATAAAG
;
; Matrix parameters
; Number of sites 12
; Columns 16
; 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 TAMCYMWWWMGTRGTR
; AC TAMCYMWWWMGTRGTR
; id TAMCYMWWWMGTRGTR
; name TAMCYMWWWMGTRGTR
; description TamCymwwamGkrGtr
; statistical_basis 12 sequences
; sites 12
; nb_sites 12
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 7.04636
; information.per.column 0.440397
; max.possible.info.per.col 1.58952
; consensus.strict TacCccaaacGtgGta
; consensus.strict.rc TACCACGTTTGGGGTA
; consensus.IUPAC TamCymwwamGkrGtr
; consensus.IUPAC.rc YACYMCKTWWKRGKTA
; consensus.regexp Ta[ac]C[ct][ac][at][at]a[ac]G[gt][ag]Gt[ag]
; consensus.regexp.rc [CT]AC[CT][AC]C[GT]T[AT][AT][GT][AG]G[GT]TA
; residues.content.crude.freq a:0.3281|c:0.2135|g:0.1823|t:0.2760
; G+C.content.crude.freq 0.395833
; residues.content.corrected.freq a:0.3253|c:0.2131|g:0.1840|t:0.2777
; G+C.content.corrected.freq 0.397064
; min(P(S|M)) 6.34067e-27
; max(P(S|M)) 0.000147746
; proba_range 0.000147746
; Wmin -36.4
; Wmax 13.1
; Wrange 49.5
; logo file:/NarP.EcolK12_2nt_upstream.16.meme_quality_logo_m1.png
; logo file:/NarP.EcolK12_2nt_upstream.16.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161045
; Job done 2019-06-03.161045
; Seconds 0.52
; user 0.52
; system 0.06
; cuser 0.39
; csystem 0.04