RegulonDB
FhlA matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/FhlA/FhlA.EcolK12_1nt_upstream.17.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 /FhlA.EcolK12_1nt_upstream.17.meme_quality_logo
; Input files
; input /FhlA.EcolK12_1nt_upstream.17.meme_quality_matrix.tf
; prior /FhlA.EcolK12_1nt_upstream.17.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /FhlA.EcolK12_1nt_upstream.17.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 3 0 1 0 0 3 1 0 0 1 0 0 5 1 2 1 2
C 1 2 1 1 6 3 0 0 1 0 5 0 2 5 0 1 1
G 1 1 4 3 0 0 4 0 2 0 0 7 0 1 5 1 3
T 2 4 1 3 1 1 2 7 4 6 2 0 0 0 0 4 1
//
A 0.4 0.0 0.2 0.0 0.0 0.4 0.2 0.0 0.0 0.2 0.0 0.0 0.7 0.2 0.3 0.2 0.3
C 0.2 0.3 0.2 0.2 0.8 0.4 0.0 0.0 0.2 0.0 0.7 0.0 0.3 0.7 0.0 0.2 0.2
G 0.2 0.2 0.5 0.4 0.0 0.0 0.5 0.0 0.3 0.0 0.0 0.9 0.0 0.2 0.7 0.2 0.4
T 0.3 0.5 0.2 0.4 0.2 0.2 0.3 0.9 0.5 0.8 0.3 0.0 0.0 0.0 0.0 0.5 0.2
//
A 0.3 -2.1 -0.6 -2.1 -2.1 0.3 -0.6 -2.1 -2.1 -0.6 -2.1 -2.1 0.8 -0.6 -0.0 -0.6 -0.0
C -0.3 0.3 -0.3 -0.3 1.3 0.7 -2.1 -2.1 -0.3 -2.1 1.1 -2.1 0.3 1.1 -2.1 -0.3 -0.3
G -0.3 -0.3 0.9 0.7 -2.1 -2.1 0.9 -2.1 0.3 -2.1 -2.1 1.5 -2.1 -0.3 1.2 -0.3 0.7
T -0.0 0.6 -0.6 0.3 -0.6 -0.6 -0.0 1.1 0.6 1.0 -0.0 -2.1 -2.1 -2.1 -2.1 0.6 -0.6
//
A 0.1 -0.1 -0.1 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.5 -0.1 -0.0 -0.1 -0.0
C -0.0 0.1 -0.0 -0.0 1.0 0.3 -0.1 -0.1 -0.0 -0.1 0.7 -0.1 0.1 0.7 -0.1 -0.0 -0.0
G -0.0 -0.0 0.5 0.3 -0.1 -0.1 0.5 -0.1 0.1 -0.1 -0.1 1.3 -0.1 -0.0 0.8 -0.0 0.3
T -0.0 0.3 -0.1 0.1 -0.1 -0.1 -0.0 1.0 0.3 0.8 -0.0 -0.1 -0.1 -0.1 -0.1 0.3 -0.1
//
; Sites 7
>site_0
GTCGCCGTGTCGACGTG
>site_1
TCGTCAGTTTTGACGTG
>site_2
ATGTCATTTTCGACACT
>site_3
TTGTCATTTTTGACGAA
>site_4
ACACCCGTGTCGCAGGG
>site_5
ATGGCTGTCACGCGGTA
>site_6
CGTGTCATTTCGACATC
;
; Matrix parameters
; Number of sites 7
; Columns 17
; 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 WYGKCMKTKTCGACGTR
; AC WYGKCMKTKTCGACGTR
; id WYGKCMKTKTCGACGTR
; name WYGKCMKTKTCGACGTR
; description aygkCmgTktCGmCGtg
; statistical_basis 7 sequences
; sites 7
; nb_sites 7
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 7.53676
; information.per.column 0.443339
; max.possible.info.per.col 1.58873
; consensus.strict atggCcgTttCGaCGtg
; consensus.strict.rc CACGTCGAAACGGCCAT
; consensus.IUPAC aygkCmgTktCGmCGtg
; consensus.IUPAC.rc CACGKCGAMACKGMCRT
; consensus.regexp a[ct]g[gt]C[ac]gT[gt]tCG[ac]CGtg
; consensus.regexp.rc CACG[GT]CGA[AC]AC[GT]G[AC]C[AG]T
; residues.content.crude.freq a:0.1681|c:0.2437|g:0.2689|t:0.3193
; G+C.content.crude.freq 0.512605
; residues.content.corrected.freq a:0.1834|c:0.2392|g:0.2608|t:0.3166
; G+C.content.corrected.freq 0.499998
; min(P(S|M)) 4.45498e-24
; max(P(S|M)) 0.000109376
; proba_range 0.000109376
; Wmin -29.2
; Wmax 15.2
; Wrange 44.4
; logo file:/FhlA.EcolK12_1nt_upstream.17.meme_quality_logo_m1.png
; logo file:/FhlA.EcolK12_1nt_upstream.17.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.61
; user 0.61
; system 0.06
; cuser 0.42
; csystem 0.05