RegulonDB
RhaS matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/RhaS/RhaS.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 /RhaS.EcolK12_1nt_upstream.20.meme_quality_logo
; Input files
; input /RhaS.EcolK12_1nt_upstream.20.meme_quality_matrix.tf
; prior /RhaS.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 /RhaS.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 2 0 0 0 1 4 4 1 4 6 1 4 3 3 4 2 1 5 4 0
C 4 2 1 0 7 2 0 3 4 0 5 0 0 2 2 1 0 0 0 1
G 0 0 4 4 0 2 4 1 0 1 2 4 5 3 1 1 4 1 1 6
T 2 6 3 4 0 0 0 3 0 1 0 0 0 0 1 4 3 2 3 1
//
A 0.3 0.0 0.0 0.0 0.1 0.5 0.5 0.1 0.5 0.7 0.1 0.5 0.4 0.4 0.5 0.3 0.1 0.6 0.5 0.0
C 0.5 0.2 0.1 0.0 0.8 0.2 0.0 0.4 0.5 0.0 0.6 0.0 0.0 0.2 0.2 0.1 0.0 0.0 0.0 0.1
G 0.0 0.0 0.5 0.5 0.0 0.2 0.5 0.1 0.0 0.1 0.2 0.5 0.6 0.4 0.1 0.1 0.5 0.1 0.1 0.7
T 0.3 0.7 0.4 0.5 0.0 0.0 0.0 0.4 0.0 0.1 0.0 0.0 0.0 0.0 0.1 0.5 0.4 0.3 0.4 0.1
//
A -0.1 -2.2 -2.2 -2.2 -0.7 0.5 0.5 -0.7 0.5 0.9 -0.7 0.5 0.2 0.2 0.5 -0.1 -0.7 0.7 0.5 -2.2
C 0.8 0.2 -0.4 -2.2 1.4 0.2 -2.2 0.5 0.8 -2.2 1.0 -2.2 -2.2 0.2 0.2 -0.4 -2.2 -2.2 -2.2 -0.4
G -2.2 -2.2 0.8 0.8 -2.2 0.2 0.8 -0.4 -2.2 -0.4 0.2 0.8 1.0 0.6 -0.4 -0.4 0.8 -0.4 -0.4 1.2
T -0.2 0.9 0.2 0.5 -2.2 -2.2 -2.2 0.2 -2.2 -0.7 -2.2 -2.2 -2.2 -2.2 -0.7 0.5 0.2 -0.2 0.2 -0.7
//
A -0.0 -0.1 -0.1 -0.1 -0.1 0.2 0.2 -0.1 0.2 0.6 -0.1 0.2 0.1 0.1 0.2 -0.0 -0.1 0.4 0.2 -0.1
C 0.4 0.0 -0.1 -0.1 1.1 0.0 -0.1 0.2 0.4 -0.1 0.6 -0.1 -0.1 0.0 0.0 -0.1 -0.1 -0.1 -0.1 -0.1
G -0.0 -0.0 0.4 0.4 -0.0 0.0 0.4 -0.1 -0.0 -0.1 0.0 0.4 0.6 0.2 -0.1 -0.1 0.4 -0.1 -0.1 0.8
T -0.0 0.6 0.1 0.2 -0.1 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.2 0.1 -0.0 0.1 -0.1
//
; Sites 8
>site_0
CTGGCAATCACGGCATTAAG
>site_1
TTGGCAACCAGGGAAAGATG
>site_2
CTTTCCAGAACAGGCTGTGG
>site_3
ACGGCGGCAACAGGCGAAAG
>site_4
CTGTCAGTAACGAGAAGGTC
>site_5
ACCTCGGCCAGAGAACGAAG
>site_6
TTTTCCGTCGAAAATTTAAG
>site_7
CTTGAAAAATCGACGTTTTT
;
; Matrix parameters
; Number of sites 8
; 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 HTKKCVRYMACRRVMWKAWG
; AC HTKKCVRYMACRRVMWKAWG
; id HTKKCVRYMACRRVMWKAWG
; name HTKKCVRYMACRRVMWKAWG
; description cykkCvrymaSrRvmtkawG
; statistical_basis 8 sequences
; sites 8
; nb_sites 8
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 7.56534
; information.per.column 0.378267
; max.possible.info.per.col 1.58873
; consensus.strict ctggCagccaCgGgatgaaG
; consensus.strict.rc CTTCATCCCGTGGCTGCCAG
; consensus.IUPAC cykkCvrymaSrRvmtkawG
; consensus.IUPAC.rc CWTMAKBYYSTKRYBGMMRG
; consensus.regexp c[ct][gt][gt]C[acg][ag][ct][ac]a[CG][ag][AG][acg][ac]t[gt]a[at]G
; consensus.regexp.rc C[AT]T[AC]A[GT][CGT][CT][CT][CG]T[GT][AG][CT][CGT]G[AC][AC][AG]G
; residues.content.crude.freq a:0.3063|c:0.2125|g:0.2750|t:0.2062
; G+C.content.crude.freq 0.4875
; residues.content.corrected.freq a:0.3045|c:0.2120|g:0.2671|t:0.2164
; G+C.content.corrected.freq 0.479083
; min(P(S|M)) 1.91317e-30
; max(P(S|M)) 1.94353e-06
; proba_range 1.94353e-06
; Wmin -39.3
; Wmax 15.9
; Wrange 55.2
; logo file:/RhaS.EcolK12_1nt_upstream.20.meme_quality_logo_m1.png
; logo file:/RhaS.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 0.52
; user 0.52
; system 0.05
; cuser 0.44
; csystem 0.04