RegulonDB
LeuO matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/LeuO/LeuO.EcolK12_1nt_upstream.23.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 /LeuO.EcolK12_1nt_upstream.23.meme_quality_logo
; Input files
; input /LeuO.EcolK12_1nt_upstream.23.meme_quality_matrix.tf
; prior /LeuO.EcolK12_1nt_upstream.23.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /LeuO.EcolK12_1nt_upstream.23.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 9 0 4 4 5 1 7 2 3 4 0 1 9 8 1 4 2 4 4 3 3 3 2
C 0 0 1 3 1 1 2 4 3 0 1 0 0 0 0 0 1 0 1 1 0 0 4
G 0 0 0 1 1 0 0 0 2 5 1 8 1 1 0 0 3 0 1 0 2 2 1
T 1 10 5 2 3 8 1 4 2 1 8 1 0 1 9 6 4 6 4 6 5 5 3
//
A 0.8 0.0 0.4 0.4 0.5 0.1 0.7 0.2 0.3 0.4 0.0 0.1 0.8 0.8 0.1 0.4 0.2 0.4 0.4 0.3 0.3 0.3 0.2
C 0.0 0.0 0.1 0.3 0.1 0.1 0.2 0.4 0.3 0.0 0.1 0.0 0.0 0.0 0.0 0.0 0.1 0.0 0.1 0.1 0.0 0.0 0.4
G 0.0 0.0 0.0 0.1 0.1 0.0 0.0 0.0 0.2 0.5 0.1 0.7 0.1 0.1 0.0 0.0 0.3 0.0 0.1 0.0 0.2 0.2 0.1
T 0.1 0.9 0.5 0.2 0.3 0.8 0.1 0.4 0.2 0.1 0.8 0.1 0.0 0.1 0.8 0.6 0.4 0.6 0.4 0.6 0.5 0.5 0.3
//
A 1.1 -2.4 0.3 0.3 0.5 -0.9 0.8 -0.3 0.0 0.3 -2.4 -0.9 1.1 1.0 -0.9 0.3 -0.3 0.3 0.3 0.0 0.0 0.0 -0.3
C -2.4 -2.4 -0.6 0.3 -0.6 -0.6 -0.0 0.6 0.3 -2.4 -0.6 -2.4 -2.4 -2.4 -2.4 -2.4 -0.6 -2.4 -0.6 -0.6 -2.4 -2.4 0.6
G -2.4 -2.4 -2.4 -0.6 -0.6 -2.4 -2.4 -2.4 -0.0 0.8 -0.6 1.3 -0.6 -0.6 -2.4 -2.4 0.4 -2.4 -0.6 -2.4 -0.0 -0.0 -0.6
T -0.9 1.1 0.5 -0.4 0.0 0.9 -0.9 0.3 -0.4 -0.9 0.9 -0.9 -2.4 -0.9 1.0 0.7 0.3 0.7 0.3 0.7 0.5 0.5 0.0
//
A 0.9 -0.1 0.1 0.1 0.2 -0.1 0.5 -0.1 0.0 0.1 -0.1 -0.1 0.9 0.7 -0.1 0.1 -0.1 0.1 0.1 0.0 0.0 0.0 -0.1
C -0.0 -0.0 -0.1 0.1 -0.1 -0.1 -0.0 0.2 0.1 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.1 -0.1 -0.0 -0.0 0.2
G -0.0 -0.0 -0.0 -0.1 -0.1 -0.0 -0.0 -0.0 -0.0 0.4 -0.1 1.0 -0.1 -0.1 -0.0 -0.0 0.1 -0.0 -0.1 -0.0 -0.0 -0.0 -0.1
T -0.1 1.1 0.2 -0.1 0.0 0.7 -0.1 0.1 -0.1 -0.1 0.7 -0.1 -0.1 -0.1 0.9 0.4 0.1 0.4 0.1 0.4 0.2 0.2 0.0
//
; Sites 10
>site_0
ATAATTACCATGAATTTTATTAC
>site_1
ATTCATACTGTGAATATAAAATC
>site_2
ATTTGTCTGGTGAATTATTTGTC
>site_3
ATTAAACCAATGAATATATTTTT
>site_4
ATTGATTTGGTGAATATTATTGA
>site_5
ATAACTACCGCGAATACTCAATC
>site_6
ATTCTTAACATTAATTGATCAAT
>site_7
TTAATTATTGGGATTTGTTATAT
>site_8
ATCTACAAAATGGATTAAATGTG
>site_9
ATACATATATTAAGATGTGTTGA
;
; Matrix parameters
; Number of sites 10
; Columns 23
; 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 ATWHWTAHNRTGAATWDWWWWWH
; AC ATWHWTAHNRTGAATWDWWWWWH
; id ATWHWTAHNRTGAATWDWWWWWH
; name ATWHWTAHNRTGAATWDWWWWWH
; description ATwmwtaymrtGAaTwkwwwwwy
; statistical_basis 10 sequences
; sites 10
; nb_sites 10
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 8.32556
; information.per.column 0.361981
; max.possible.info.per.col 1.58873
; consensus.strict ATtcataccgtGAaTtgtatttc
; consensus.strict.rc GAAATACAATTCACGGTATGAAT
; consensus.IUPAC ATwmwtaymrtGAaTwkwwwwwy
; consensus.IUPAC.rc RWWWWWMWATTCAYKRTAWKWAT
; consensus.regexp AT[at][ac][at]ta[ct][ac][ag]tGAaT[at][gt][at][at][at][at][at][ct]
; consensus.regexp.rc [AG][AT][AT][AT][AT][AT][AC][AT]ATTCA[CT][GT][AG]TA[AT][GT][AT]AT
; residues.content.crude.freq a:0.3609|c:0.1000|g:0.1261|t:0.4130
; G+C.content.crude.freq 0.226087
; residues.content.corrected.freq a:0.3545|c:0.1098|g:0.1332|t:0.4025
; G+C.content.corrected.freq 0.242965
; min(P(S|M)) 1.83143e-35
; max(P(S|M)) 1.51874e-06
; proba_range 1.51874e-06
; Wmin -44.3
; Wmax 16.6
; Wrange 60.9
; logo file:/LeuO.EcolK12_1nt_upstream.23.meme_quality_logo_m1.png
; logo file:/LeuO.EcolK12_1nt_upstream.23.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161000
; Job done 2019-06-03.161000
; Seconds 0.58
; user 0.58
; system 0.06
; cuser 0.44
; csystem 0.04