RegulonDB
UlaR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/UlaR/UlaR.EcolK12_2nt_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 /UlaR.EcolK12_2nt_upstream.23.meme_quality_logo
; Input files
; input /UlaR.EcolK12_2nt_upstream.23.meme_quality_matrix.tf
; prior /UlaR.EcolK12_2nt_upstream.23.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /UlaR.EcolK12_2nt_upstream.23.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 1 0 4 0 0 2 0 1 1 1 0 0 4 2 1 3 3 1 1 1 1 0 3
C 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 2 1 0 0 0
G 0 4 0 0 0 1 2 0 0 0 0 4 0 0 0 0 0 0 0 2 0 4 0
T 3 0 0 4 4 0 1 3 3 3 4 0 0 2 2 1 1 3 1 0 3 0 1
//
A 0.3 0.1 0.9 0.1 0.1 0.5 0.1 0.3 0.3 0.3 0.1 0.1 0.9 0.5 0.3 0.7 0.7 0.3 0.3 0.3 0.3 0.1 0.7
C 0.0 0.0 0.0 0.0 0.0 0.2 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.4 0.2 0.0 0.0 0.0
G 0.0 0.8 0.0 0.0 0.0 0.2 0.4 0.0 0.0 0.0 0.0 0.8 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.4 0.0 0.8 0.0
T 0.7 0.1 0.1 0.9 0.9 0.1 0.3 0.7 0.7 0.7 0.9 0.1 0.1 0.5 0.5 0.3 0.3 0.7 0.3 0.1 0.7 0.1 0.3
//
A -0.1 -1.6 1.1 -1.6 -1.6 0.5 -1.6 -0.1 -0.1 -0.1 -1.6 -1.6 1.1 0.5 -0.1 0.8 0.8 -0.1 -0.1 -0.1 -0.1 -1.6 0.8
C -1.6 -1.6 -1.6 -1.6 -1.6 0.2 0.2 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 0.2 -1.6 -1.6 -1.6 0.8 0.2 -1.6 -1.6 -1.6
G -1.6 1.4 -1.6 -1.6 -1.6 0.2 0.8 -1.6 -1.6 -1.6 -1.6 1.4 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 0.8 -1.6 1.4 -1.6
T 0.8 -1.6 -1.6 1.1 1.1 -1.6 -0.1 0.8 0.8 0.8 1.1 -1.6 -1.6 0.4 0.4 -0.1 -0.1 0.8 -0.1 -1.6 0.8 -1.6 -0.1
//
A -0.0 -0.1 0.9 -0.1 -0.1 0.2 -0.1 -0.0 -0.0 -0.0 -0.1 -0.1 0.9 0.2 -0.0 0.5 0.5 -0.0 -0.0 -0.0 -0.0 -0.1 0.5
C -0.1 -0.1 -0.1 -0.1 -0.1 0.0 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.0 -0.1 -0.1 -0.1 0.3 0.0 -0.1 -0.1 -0.1
G -0.1 1.2 -0.1 -0.1 -0.1 0.0 0.3 -0.1 -0.1 -0.1 -0.1 1.2 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.3 -0.1 1.2 -0.1
T 0.5 -0.1 -0.1 0.9 0.9 -0.1 -0.0 0.5 0.5 0.5 0.9 -0.1 -0.1 0.2 0.2 -0.0 -0.0 0.5 -0.0 -0.1 0.5 -0.1 -0.0
//
; Sites 4
>site_0
TGATTGGTTTTGATTAATCCTGA
>site_1
TGATTCGAATTGAACTATCATGA
>site_2
AGATTATTTATGATTAAATGTGA
>site_3
TGATTACTTTTGAAAATTAGAGT
;
; Matrix parameters
; Number of sites 4
; Columns 23
; 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 TGATTVBTTTTGAWHAATHVTGA
; AC TGATTVBTTTTGAWHAATHVTGA
; id TGATTVBTTTTGAWHAATHVTGA
; name TGATTVBTTTTGAWHAATHVTGA
; description tGATTvstttTGAwyaatcstGa
; statistical_basis 4 sequences
; sites 4
; nb_sites 4
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 10.8465
; information.per.column 0.471586
; max.possible.info.per.col 1.58952
; consensus.strict tGATTagtttTGAataatcgtGa
; consensus.strict.rc TCACGATTATTCAAAACTAATCA
; consensus.IUPAC tGATTvstttTGAwyaatcstGa
; consensus.IUPAC.rc TCASGATTRWTCAAAASBAATCA
; consensus.regexp tGATT[acg][cg]tttTGA[at][ct]aatc[cg]tGa
; consensus.regexp.rc TCA[CG]GATT[AG][AT]TCAAAA[CG][CGT]AATCA
; residues.content.crude.freq a:0.3261|c:0.0652|g:0.1848|t:0.4239
; G+C.content.crude.freq 0.25
; residues.content.corrected.freq a:0.3191|c:0.0937|g:0.1886|t:0.3985
; G+C.content.corrected.freq 0.282367
; min(P(S|M)) 3.55599e-32
; max(P(S|M)) 5.40607e-05
; proba_range 5.40607e-05
; Wmin -37.1
; Wmax 20.5
; Wrange 57.6
; logo file:/UlaR.EcolK12_2nt_upstream.23.meme_quality_logo_m1.png
; logo file:/UlaR.EcolK12_2nt_upstream.23.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161114
; Job done 2019-06-03.161115
; Seconds 0.58
; user 0.58
; system 0.06
; cuser 0.41
; csystem 0.04