RegulonDB
BaeR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/BaeR/BaeR.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 /BaeR.EcolK12_1nt_upstream.23.meme_quality_logo
; Input files
; input /BaeR.EcolK12_1nt_upstream.23.meme_quality_matrix.tf
; prior /BaeR.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 /BaeR.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 0 0 2 0 1 0 0 0 0 0 0 0 3 0 2 4 0 0 0 0 0 0 0
C 3 1 0 0 0 0 0 0 4 0 3 4 1 1 0 0 0 1 0 1 3 0 3
G 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 3 3 0 2 1
T 0 3 2 4 3 3 4 4 0 4 1 0 0 3 1 0 4 3 1 0 1 2 0
//
A 0.1 0.1 0.5 0.1 0.3 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.7 0.1 0.5 0.9 0.1 0.1 0.1 0.1 0.1 0.1 0.1
C 0.6 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.8 0.0 0.6 0.8 0.2 0.2 0.0 0.0 0.0 0.2 0.0 0.2 0.6 0.0 0.6
G 0.2 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.6 0.6 0.0 0.4 0.2
T 0.1 0.7 0.5 0.9 0.7 0.7 0.9 0.9 0.1 0.9 0.3 0.1 0.1 0.7 0.3 0.1 0.9 0.7 0.3 0.1 0.3 0.5 0.1
//
A -1.6 -1.6 0.5 -1.6 -0.1 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 0.8 -1.6 0.5 1.1 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6
C 1.1 0.2 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 1.4 -1.6 1.1 1.4 0.2 0.2 -1.6 -1.6 -1.6 0.2 -1.6 0.2 1.1 -1.6 1.1
G 0.2 -1.6 -1.6 -1.6 -1.6 0.2 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 0.2 -1.6 -1.6 -1.6 1.1 1.1 -1.6 0.8 0.2
T -1.6 0.8 0.4 1.1 0.8 0.8 1.1 1.1 -1.6 1.1 -0.1 -1.6 -1.6 0.8 -0.1 -1.6 1.1 0.8 -0.1 -1.6 -0.1 0.4 -1.6
//
A -0.1 -0.1 0.2 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.5 -0.1 0.2 0.9 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
C 0.7 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 1.2 -0.1 0.7 1.2 0.0 0.0 -0.1 -0.1 -0.1 0.0 -0.1 0.0 0.7 -0.1 0.7
G 0.0 -0.1 -0.1 -0.1 -0.1 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.0 -0.1 -0.1 -0.1 0.7 0.7 -0.1 0.3 0.0
T -0.1 0.5 0.2 0.9 0.5 0.5 0.9 0.9 -0.1 0.9 -0.0 -0.1 -0.1 0.5 -0.0 -0.1 0.9 0.5 -0.0 -0.1 -0.0 0.2 -0.1
//
; Sites 4
>site_0
CTTTTTTTCTCCATAATTGGCGC
>site_1
CTTTTTTTCTCCACGATTGGCTC
>site_2
CCATTTTTCTCCCTTATTGGCTG
>site_3
GTATAGTTCTTCATAATCTCTGC
;
; Matrix parameters
; Number of sites 4
; 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 CTWTTTTTCTCCATDATTGGCKC
; AC CTWTTTTTCTCCATDATTGGCKC
; id CTWTTTTTCTCCATDATTGGCKC
; name CTWTTTTTCTCCATDATTGGCKC
; description SywTtkTTCTCCmyrATyGSCkS
; statistical_basis 4 sequences
; sites 4
; nb_sites 4
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 12.4875
; information.per.column 0.542937
; max.possible.info.per.col 1.58873
; consensus.strict CtaTttTTCTCCataATtGGCgC
; consensus.strict.rc GCGCCAATTATGGAGAAAAATAG
; consensus.IUPAC SywTtkTTCTCCmyrATyGSCkS
; consensus.IUPAC.rc SMGSCRATYRKGGAGAAMAAWRS
; consensus.regexp [CG][ct][at]Tt[gt]TTCTCC[ac][ct][ag]AT[ct]G[CG]C[gt][CG]
; consensus.regexp.rc [CG][AC]G[CG]C[AG]AT[CT][AG][GT]GGAGAA[AC]AA[AT][AG][CG]
; residues.content.crude.freq a:0.1304|c:0.2717|g:0.1304|t:0.4674
; G+C.content.crude.freq 0.402174
; residues.content.corrected.freq a:0.1625|c:0.2589|g:0.1452|t:0.4334
; G+C.content.corrected.freq 0.404088
; min(P(S|M)) 3.49953e-32
; max(P(S|M)) 0.000157402
; proba_range 0.000157402
; Wmin -37.1
; Wmax 22.5
; Wrange 59.6
; logo file:/BaeR.EcolK12_1nt_upstream.23.meme_quality_logo_m1.png
; logo file:/BaeR.EcolK12_1nt_upstream.23.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 0.05
; cuser 0.43
; csystem 0.05