RegulonDB
CaiF matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/CaiF/CaiF.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 /CaiF.EcolK12_1nt_upstream.19.meme_quality_logo
; Input files
; input /CaiF.EcolK12_1nt_upstream.19.meme_quality_matrix.tf
; prior /CaiF.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 /CaiF.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 1 4 2 0 4 4 0 4 0 0 0 4 4 4 2 0 1 1 0
C 2 0 2 4 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1
G 0 0 0 0 0 0 0 0 0 0 4 0 0 0 2 0 0 1 3
T 1 0 0 0 0 0 4 0 4 4 0 0 0 0 0 3 2 1 0
//
A 0.3 0.9 0.5 0.1 0.9 0.9 0.1 0.9 0.1 0.1 0.1 0.9 0.9 0.9 0.5 0.1 0.3 0.3 0.1
C 0.4 0.0 0.4 0.8 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.2 0.2 0.2
G 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.8 0.0 0.0 0.0 0.4 0.0 0.0 0.2 0.6
T 0.3 0.1 0.1 0.1 0.1 0.1 0.9 0.1 0.9 0.9 0.1 0.1 0.1 0.1 0.1 0.7 0.5 0.3 0.1
//
A -0.1 1.1 0.5 -1.6 1.1 1.1 -1.6 1.1 -1.6 -1.6 -1.6 1.1 1.1 1.1 0.5 -1.6 -0.1 -0.1 -1.6
C 0.8 -1.6 0.8 1.4 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 0.2 0.2 0.2 0.2
G -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 1.4 -1.6 -1.6 -1.6 0.8 -1.6 -1.6 0.2 1.1
T -0.1 -1.6 -1.6 -1.6 -1.6 -1.6 1.1 -1.6 1.1 1.1 -1.6 -1.6 -1.6 -1.6 -1.6 0.8 0.4 -0.1 -1.6
//
A -0.0 0.9 0.2 -0.1 0.9 0.9 -0.1 0.9 -0.1 -0.1 -0.1 0.9 0.9 0.9 0.2 -0.1 -0.0 -0.0 -0.1
C 0.3 -0.1 0.3 1.2 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.0 0.0 0.0 0.0
G -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 1.2 -0.1 -0.1 -0.1 0.3 -0.1 -0.1 0.0 0.7
T -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 0.9 -0.1 0.9 0.9 -0.1 -0.1 -0.1 -0.1 -0.1 0.5 0.2 -0.0 -0.1
//
; Sites 4
>site_0
CACCAATATTGAAAGTCAG
>site_1
TAACAATATTGAAAGTTGG
>site_2
CACCAATATTGAAAACACG
>site_3
AAACAATATTGAAAATTTC
;
; Matrix parameters
; Number of sites 4
; 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 HAMCAATATTGAAARTHNG
; AC HAMCAATATTGAAARTHNG
; id HAMCAATATTGAAARTHNG
; name HAMCAATATTGAAARTHNG
; description cAmCAATATTGAAAryysS
; statistical_basis 4 sequences
; sites 4
; nb_sites 4
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 10.9149
; information.per.column 0.574469
; max.possible.info.per.col 1.58873
; consensus.strict cAcCAATATTGAAAgttgG
; consensus.strict.rc CCAACTTTCAATATTGGTG
; consensus.IUPAC cAmCAATATTGAAAryysS
; consensus.IUPAC.rc SSRRYTTTCAATATTGKTG
; consensus.regexp cA[ac]CAATATTGAAA[ag][ct][ct][cg][CG]
; consensus.regexp.rc [CG][CG][AG][AG][CT]TTTCAATATTG[GT]TG
; residues.content.crude.freq a:0.4605|c:0.1579|g:0.1316|t:0.2500
; G+C.content.crude.freq 0.289474
; residues.content.corrected.freq a:0.4266|c:0.1678|g:0.1461|t:0.2595
; G+C.content.corrected.freq 0.313928
; min(P(S|M)) 3.53747e-26
; max(P(S|M)) 0.000719156
; proba_range 0.000719156
; Wmin -29.2
; Wmax 18.4
; Wrange 47.6
; logo file:/CaiF.EcolK12_1nt_upstream.19.meme_quality_logo_m1.png
; logo file:/CaiF.EcolK12_1nt_upstream.19.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.59
; user 0.59
; system 0.05
; cuser 0.42
; csystem 0.04