RegulonDB
RcsAB matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/RcsAB/RcsAB.EcolK12_2nt_upstream.18.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 /RcsAB.EcolK12_2nt_upstream.18.meme_quality_logo
; Input files
; input /RcsAB.EcolK12_2nt_upstream.18.meme_quality_matrix.tf
; prior /RcsAB.EcolK12_2nt_upstream.18.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /RcsAB.EcolK12_2nt_upstream.18.meme_quality_matrix_info.txt
; Output format tab
; pseudo-weight 1
; Background model
; Strand undef
; Background pseudo-frequency 0.01
; Residue probabilities
; a 0.29114
; c 0.20781
; g 0.20402
; t 0.29702
A 0 0 5 6 1 1 2 1 3 4 0 0 0 2 5 4 6 4
C 3 0 0 0 0 0 0 1 1 1 0 4 6 0 1 0 0 0
G 1 0 1 0 4 4 2 0 0 0 0 0 0 1 0 0 0 0
T 2 6 0 0 1 1 2 4 2 1 6 2 0 3 0 2 0 2
//
A 0.0 0.0 0.8 0.9 0.2 0.2 0.3 0.2 0.5 0.6 0.0 0.0 0.0 0.3 0.8 0.6 0.9 0.6
C 0.5 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.2 0.2 0.0 0.6 0.9 0.0 0.2 0.0 0.0 0.0
G 0.2 0.0 0.2 0.0 0.6 0.6 0.3 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.0
T 0.3 0.9 0.0 0.0 0.2 0.2 0.3 0.6 0.3 0.2 0.9 0.3 0.0 0.5 0.0 0.3 0.0 0.3
//
A -1.9 -1.9 1.0 1.1 -0.5 -0.5 0.1 -0.5 0.5 0.7 -1.9 -1.9 -1.9 0.1 1.0 0.7 1.1 0.7
C 0.8 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 -0.2 -0.2 -0.2 -1.9 1.1 1.5 -1.9 -0.2 -1.9 -1.9 -1.9
G -0.2 -1.9 -0.2 -1.9 1.1 1.1 0.4 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 -0.2 -1.9 -1.9 -1.9 -1.9
T 0.1 1.1 -1.9 -1.9 -0.5 -0.5 0.1 0.7 0.1 -0.5 1.1 0.1 -1.9 0.5 -1.9 0.1 -1.9 0.1
//
A -0.1 -0.1 0.7 1.0 -0.1 -0.1 0.0 -0.1 0.2 0.5 -0.1 -0.1 -0.1 0.0 0.7 0.5 1.0 0.5
C 0.4 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.0 -0.0 -0.1 0.6 1.3 -0.1 -0.0 -0.1 -0.1 -0.1
G -0.0 -0.1 -0.0 -0.1 0.6 0.6 0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1
T 0.0 1.0 -0.1 -0.1 -0.1 -0.1 0.0 0.4 0.0 -0.1 1.0 0.0 -0.1 0.2 -0.1 0.0 -0.1 0.0
//
; Sites 6
>site_0
CTAAGGATTATCCGAAAA
>site_1
GTGAGGTTAATCCTAAAA
>site_2
CTAAAGAAACTCCTAAAA
>site_3
CTAAGATTTTTCCTAAAT
>site_4
TTAAGTGTCATTCAATAT
>site_5
TTAATGGCAATTCACTAA
;
; Matrix parameters
; Number of sites 6
; Columns 18
; Rows 4
; Alphabet A|C|G|T
; Prior A:0.291144263562772|C:0.207810681831126|G:0.204024081631615|T:0.297020972974487|a:0.291144263562772|c:0.207810681831126|g:0.204024081631615|t:0.297020972974487
; program transfac
; matrix.nb 1
; accession YTAAGGDTWATYCWAWAW
; AC YTAAGGDTWATYCWAWAW
; id YTAAGGDTWATYCWAWAW
; name YTAAGGDTWATYCWAWAW
; description yTaAGGdtwaTYCwawAw
; statistical_basis 6 sequences
; sites 6
; nb_sites 6
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 8.84858
; information.per.column 0.491588
; max.possible.info.per.col 1.58952
; consensus.strict cTaAGGgtaaTCCtaaAa
; consensus.strict.rc TTTTAGGATTACCCTTAG
; consensus.IUPAC yTaAGGdtwaTYCwawAw
; consensus.IUPAC.rc WTWTWGRATWAHCCTTAR
; consensus.regexp [ct]TaAGG[agt]t[at]aT[CT]C[at]a[at]A[at]
; consensus.regexp.rc [AT]T[AT]T[AT]G[AG]AT[AT]A[ACT]CCTTA[AG]
; residues.content.crude.freq a:0.4074|c:0.1574|g:0.1204|t:0.3148
; G+C.content.crude.freq 0.277778
; residues.content.corrected.freq a:0.3908|c:0.1646|g:0.1323|t:0.3123
; G+C.content.corrected.freq 0.296929
; min(P(S|M)) 3.60462e-28
; max(P(S|M)) 0.000338157
; proba_range 0.000338157
; Wmin -35.1
; Wmax 16.2
; Wrange 51.3
; logo file:/RcsAB.EcolK12_2nt_upstream.18.meme_quality_logo_m1.png
; logo file:/RcsAB.EcolK12_2nt_upstream.18.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161100
; Seconds 0.57
; user 0.57
; system 0.06
; cuser 0.42
; csystem 0.06