RegulonDB
PhoB matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/PhoB/PhoB.EcolK12_1nt_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 /PhoB.EcolK12_1nt_upstream.20.meme_quality_logo
; Input files
; input /PhoB.EcolK12_1nt_upstream.20.meme_quality_matrix.tf
; prior /PhoB.EcolK12_1nt_upstream.20.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /PhoB.EcolK12_1nt_upstream.20.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 13 5 9 4 1 15 4 22 4 8 2 3 1 12 3 3 12 6 24 7
C 3 4 3 1 2 1 20 1 3 6 3 1 1 4 4 2 2 13 1 5
G 2 4 9 2 13 4 0 1 11 0 1 3 1 9 1 14 4 4 0 11
T 8 13 5 19 10 6 2 2 8 12 20 19 23 1 18 7 8 3 1 3
//
A 0.5 0.2 0.3 0.2 0.0 0.6 0.2 0.8 0.2 0.3 0.1 0.1 0.0 0.5 0.1 0.1 0.5 0.2 0.9 0.3
C 0.1 0.2 0.1 0.0 0.1 0.0 0.7 0.0 0.1 0.2 0.1 0.0 0.0 0.2 0.2 0.1 0.1 0.5 0.0 0.2
G 0.1 0.2 0.3 0.1 0.5 0.2 0.0 0.0 0.4 0.0 0.0 0.1 0.0 0.3 0.0 0.5 0.2 0.2 0.0 0.4
T 0.3 0.5 0.2 0.7 0.4 0.2 0.1 0.1 0.3 0.5 0.8 0.7 0.9 0.0 0.7 0.3 0.3 0.1 0.0 0.1
//
A 0.5 -0.4 0.2 -0.6 -1.8 0.7 -0.6 1.0 -0.6 0.1 -1.2 -0.9 -1.8 0.4 -0.9 -0.9 0.4 -0.2 1.1 -0.1
C -0.6 -0.3 -0.6 -1.5 -0.9 -1.5 1.3 -1.5 -0.6 0.1 -0.6 -1.5 -1.5 -0.3 -0.3 -0.9 -0.9 0.9 -1.5 -0.1
G -0.9 -0.3 0.5 -0.9 0.9 -0.3 -3.3 -1.5 0.7 -3.3 -1.5 -0.5 -1.5 0.5 -1.5 0.9 -0.3 -0.3 -3.3 0.7
T 0.0 0.5 -0.4 0.9 0.2 -0.2 -1.3 -1.3 0.0 0.4 0.9 0.9 1.1 -1.8 0.8 -0.1 0.0 -0.9 -1.8 -0.9
//
A 0.3 -0.1 0.1 -0.1 -0.1 0.4 -0.1 0.9 -0.1 0.0 -0.1 -0.1 -0.1 0.2 -0.1 -0.1 0.2 -0.1 1.0 -0.0
C -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 1.0 -0.1 -0.1 0.0 -0.1 -0.1 -0.1 -0.0 -0.0 -0.1 -0.1 0.4 -0.1 -0.0
G -0.1 -0.0 0.2 -0.1 0.4 -0.0 -0.0 -0.1 0.3 -0.0 -0.1 -0.1 -0.1 0.2 -0.1 0.5 -0.0 -0.0 -0.0 0.3
T 0.0 0.2 -0.1 0.6 0.1 -0.1 -0.1 -0.1 0.0 0.2 0.7 0.6 0.9 -0.1 0.6 -0.0 0.0 -0.1 -0.1 -0.1
//
; Sites 26
>site_0
ATATGACAGTTTTATGACAG
>site_1
TTATGACAGATTTATGAAAA
>site_2
CCGTGACAACTTTATGACAG
>site_3
AGGTGACAGTTATATGTAAG
>site_4
ATGACACAATTTTGTGTCAG
>site_5
CCTTGTCATCTTTCTGACAC
>site_6
TTGTTAAAGATATATTACAG
>site_7
TTGTTGCATTTGTGTTGCAA
>site_8
TTGTTACATTTGTAAGATAG
>site_9
AGATGACAGAGTGATGACAG
>site_10
GCCTTACACTTTTGTTTCAC
>site_11
TTGTTTCATAATTGTTGCAA
>site_12
TGTTTACGCTTTTATTACAG
>site_13
GAATGGCAGACTTCCGTGAG
>site_14
ATTTTACATATTTAACAGAT
>site_15
CTACCACTTTTTTGTGACAA
>site_16
TTGTGTATGTTTTGTTCAAC
>site_17
AAAAGTTATTTTTCTGTAAT
>site_18
AATTGTAACCTTTAGGTAAA
>site_19
AAATGACAATTTTGTCATTT
>site_20
AAAATATAGATCTCCGTCAC
>site_21
ATTTTGCATAATTAATGTAA
>site_22
TGAGAGCAGCTATATAAGAG
>site_23
ATCAGCAAGCCTAGCGGCAG
>site_24
ACCGGACAGTTTTTCACGCA
>site_25
ATGTTTCCACCGCGTATAAC
;
; Matrix parameters
; Number of sites 26
; Columns 20
; 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 WTDTKACAKHTTTRTKWCAR
; AC WTDTKACAKHTTTRTKWCAR
; id WTDTKACAKHTTTRTKWCAR
; name WTDTKACAKHTTTRTKWCAR
; description wtrtkaCAkhttTrtgwcAg
; statistical_basis 26 sequences
; sites 26
; nb_sites 26
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 6.67244
; information.per.column 0.333622
; max.possible.info.per.col 1.58873
; consensus.strict atgtgaCAgtttTgtgacAg
; consensus.strict.rc CTGTCACAAAACTGTCACAT
; consensus.IUPAC wtrtkaCAkhttTrtgwcAg
; consensus.IUPAC.rc CTGWCAYAAADMTGTMAYAW
; consensus.regexp [at]t[ag]t[gt]aCA[gt][act]ttT[ag]tg[at]cAg
; consensus.regexp.rc CTG[AT]CA[CT]AAA[AGT][AC]TGT[AC]A[CT]A[AT]
; residues.content.crude.freq a:0.3038|c:0.1538|g:0.1808|t:0.3615
; G+C.content.crude.freq 0.334615
; residues.content.corrected.freq a:0.3034|c:0.1558|g:0.1816|t:0.3592
; G+C.content.corrected.freq 0.337472
; min(P(S|M)) 6.29034e-27
; max(P(S|M)) 1.20626e-05
; proba_range 1.20626e-05
; Wmin -30.7
; Wmax 15.8
; Wrange 46.5
; logo file:/PhoB.EcolK12_1nt_upstream.20.meme_quality_logo_m1.png
; logo file:/PhoB.EcolK12_1nt_upstream.20.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161100
; Seconds 0.57
; user 0.57
; system 0.04
; cuser 0.43
; csystem 0.04