RegulonDB
ArgP matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/ArgP/ArgP.EcolK12_1nt_upstream.19.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 /ArgP.EcolK12_1nt_upstream.19.meme_quality_logo
; Input files
; input /ArgP.EcolK12_1nt_upstream.19.meme_quality_matrix.tf
; prior /ArgP.EcolK12_1nt_upstream.19.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /ArgP.EcolK12_1nt_upstream.19.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 15 2 4 3 3 2 4 2 7 4 14 4 2 4 3 0 9 11 3
C 1 1 0 3 1 9 2 1 0 7 2 0 1 4 5 3 8 5 3
G 0 3 0 1 5 3 3 9 0 3 2 2 10 7 5 6 1 3 1
T 3 13 15 12 10 5 10 7 12 5 1 13 6 4 6 10 1 0 12
//
A 0.8 0.1 0.2 0.2 0.2 0.1 0.2 0.1 0.4 0.2 0.7 0.2 0.1 0.2 0.2 0.0 0.5 0.6 0.2
C 0.1 0.1 0.0 0.2 0.1 0.5 0.1 0.1 0.0 0.4 0.1 0.0 0.1 0.2 0.3 0.2 0.4 0.3 0.2
G 0.0 0.2 0.0 0.1 0.3 0.2 0.2 0.5 0.0 0.2 0.1 0.1 0.5 0.4 0.3 0.3 0.1 0.2 0.1
T 0.2 0.7 0.8 0.6 0.5 0.3 0.5 0.4 0.6 0.3 0.1 0.7 0.3 0.2 0.3 0.5 0.1 0.0 0.6
//
A 1.0 -0.9 -0.3 -0.6 -0.6 -0.9 -0.3 -0.9 0.2 -0.3 0.9 -0.3 -0.9 -0.3 -0.6 -3.0 0.5 0.7 -0.6
C -1.2 -1.2 -3.0 -0.3 -1.2 0.8 -0.6 -1.2 -3.0 0.6 -0.6 -3.0 -1.2 0.0 0.2 -0.3 0.7 0.2 -0.3
G -3.0 -0.2 -3.0 -1.2 0.2 -0.2 -0.2 0.8 -3.0 -0.2 -0.6 -0.6 0.9 0.6 0.2 0.4 -1.2 -0.2 -1.2
T -0.6 0.8 0.9 0.7 0.5 -0.1 0.5 0.2 0.7 -0.1 -1.5 0.8 0.1 -0.3 0.1 0.5 -1.5 -3.0 0.7
//
A 0.7 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.1 -0.1 0.6 -0.1 -0.1 -0.1 -0.1 -0.0 0.2 0.4 -0.1
C -0.1 -0.1 -0.0 -0.0 -0.1 0.4 -0.1 -0.1 -0.0 0.2 -0.1 -0.0 -0.1 0.0 0.1 -0.0 0.3 0.1 -0.0
G -0.0 -0.0 -0.0 -0.1 0.1 -0.0 -0.0 0.4 -0.0 -0.0 -0.1 -0.1 0.5 0.2 0.1 0.1 -0.1 -0.0 -0.1
T -0.1 0.5 0.7 0.4 0.3 -0.0 0.3 0.1 0.4 -0.0 -0.1 0.5 0.0 -0.1 0.0 0.3 -0.1 -0.0 0.4
//
; Sites 19
>site_0
ATTTGCTTTCCTGGGTCAT
>site_1
ATTTTGTGTCAGGTTGCAT
>site_2
ATTTTCCAATATGCGGCGT
>site_3
ATTAGCGGAAATTGATAAT
>site_4
AGTTTTTCTGATTGCCAAT
>site_5
AGATTATGTGATGACTCGT
>site_6
AATTTTTGTCTATGGTCAT
>site_7
TTTATCATTAATTTCTAAT
>site_8
ATTTGGTTATGAGATTACT
>site_9
CTATTCGGTTATTGTTAAA
>site_10
ATTCGCTTATATATTGACC
>site_11
AAATTGTGTCATAGTGCAG
>site_12
ATTTCTTGAACGGCATAAT
>site_13
TTTTGCAATCATTAGCAAA
>site_14
TTTCACTGATATCCCTCCC
>site_15
ACTTTTGTTCGAGTGGAGT
>site_16
ATTGATATAGATGGCTTAT
>site_17
ATTATAAGTAAAGCAGCCA
>site_18
AGACACCTTCATGATCGCC
;
; Matrix parameters
; Number of sites 19
; Columns 19
; 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 ATTTKYTKWHATKNNKMAT
; AC ATTTKYTKWHATKNNKMAT
; id ATTTKYTKWHATKNNKMAT
; name ATTTKYTKWHATKNNKMAT
; description atttkctkwcatksbkmmt
; statistical_basis 19 sequences
; sites 19
; nb_sites 19
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 5.39965
; information.per.column 0.284192
; max.possible.info.per.col 1.58873
; consensus.strict attttctgtcatgggtcat
; consensus.strict.rc ATGACCCATGACAGAAAAT
; consensus.IUPAC atttkctkwcatksbkmmt
; consensus.IUPAC.rc AKKMVSMATGWMAGMAAAT
; consensus.regexp attt[gt]ct[gt][at]cat[gt][cg][cgt][gt][ac][ac]t
; consensus.regexp.rc A[GT][GT][AC][ACG][CG][AC]ATG[AT][AC]AG[AC]AAAT
; residues.content.crude.freq a:0.2659|c:0.1551|g:0.1773|t:0.4017
; G+C.content.crude.freq 0.33241
; residues.content.corrected.freq a:0.2672|c:0.1577|g:0.1786|t:0.3964
; G+C.content.corrected.freq 0.336377
; min(P(S|M)) 3.15079e-26
; max(P(S|M)) 6.79047e-06
; proba_range 6.79047e-06
; Wmin -31.2
; Wmax 13.5
; Wrange 44.7
; logo file:/ArgP.EcolK12_1nt_upstream.19.meme_quality_logo_m1.png
; logo file:/ArgP.EcolK12_1nt_upstream.19.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.61
; user 0.61
; system 0.06
; cuser 0.44
; csystem 0.04