RegulonDB
Mlc matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/Mlc/Mlc.EcolK12_2nt_upstream.26.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 /Mlc.EcolK12_2nt_upstream.26.meme_quality_logo
; Input files
; input /Mlc.EcolK12_2nt_upstream.26.meme_quality_matrix.tf
; prior /Mlc.EcolK12_2nt_upstream.26.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /Mlc.EcolK12_2nt_upstream.26.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 5 3 1 0 5 0 0 0 0 4 2 3 0 1 0 0 0 4 7 7 2 2 6 4 1 2
C 0 0 0 0 0 0 0 0 1 0 3 1 2 3 0 6 0 0 0 0 0 0 0 1 0 1
G 2 2 0 0 0 0 0 0 0 3 2 1 3 0 3 0 7 0 0 0 0 0 0 0 0 4
T 0 2 6 7 2 7 7 7 6 0 0 2 2 3 4 1 0 3 0 0 5 5 1 2 6 0
//
A 0.7 0.4 0.2 0.0 0.7 0.0 0.0 0.0 0.0 0.5 0.3 0.4 0.0 0.2 0.0 0.0 0.0 0.5 0.9 0.9 0.3 0.3 0.8 0.5 0.2 0.3
C 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.4 0.2 0.3 0.4 0.0 0.8 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.2
G 0.3 0.3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.4 0.3 0.2 0.4 0.0 0.4 0.0 0.9 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5
T 0.0 0.3 0.8 0.9 0.3 0.9 0.9 0.9 0.8 0.0 0.0 0.3 0.3 0.4 0.5 0.2 0.0 0.4 0.0 0.0 0.7 0.7 0.2 0.3 0.8 0.0
//
A 0.8 0.3 -0.6 -2.1 0.8 -2.1 -2.1 -2.1 -2.1 0.6 -0.0 0.3 -2.1 -0.6 -2.1 -2.1 -2.1 0.6 1.1 1.1 -0.0 -0.0 1.0 0.6 -0.6 -0.0
C -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 -0.3 -2.1 0.7 -0.3 0.3 0.7 -2.1 1.3 -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 -0.3 -2.1 -0.3
G 0.3 0.3 -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 0.7 0.3 -0.3 0.7 -2.1 0.7 -2.1 1.5 -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 0.9
T -2.1 -0.0 1.0 1.1 -0.0 1.1 1.1 1.1 1.0 -2.1 -2.1 -0.0 -0.0 0.3 0.6 -0.6 -2.1 0.3 -2.1 -2.1 0.8 0.8 -0.6 -0.0 1.0 -2.1
//
A 0.5 0.1 -0.1 -0.1 0.5 -0.1 -0.1 -0.1 -0.1 0.3 -0.0 0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.3 1.0 1.0 -0.0 -0.0 0.8 0.3 -0.1 -0.0
C -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 0.3 -0.0 0.1 0.3 -0.1 1.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0
G 0.1 0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.3 0.1 -0.0 0.3 -0.1 0.3 -0.1 1.3 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.5
T -0.1 -0.0 0.8 1.0 -0.0 1.0 1.0 1.0 0.8 -0.1 -0.1 -0.0 -0.0 0.1 0.3 -0.1 -0.1 0.1 -0.1 -0.1 0.5 0.5 -0.1 -0.0 0.8 -0.1
//
; Sites 7
>site_0
AGTTTTTTTAAAGCTCGTAATTAATG
>site_1
AATTATTTTGATGCGCGAAATTAATC
>site_2
ATTTTTTTTGCGCTTCGTAATTAATG
>site_3
AATTATTTTACTCTGTGTAATAAATA
>site_4
GATTATTTCGGAGCGCGAAAATATAG
>site_5
ATTTATTTTAGATATCGAAAAAATTA
>site_6
GGATATTTTACCTTTCGAAATTTCTG
;
; Matrix parameters
; Number of sites 7
; Columns 26
; 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 ADTTATTTTRVWBYKCGWAATTAWTR
; AC ADTTATTTTRVWBYKCGWAATTAWTR
; id ADTTATTTTRVWBYKCGWAATTAWTR
; name ADTTATTTTRVWBYKCGWAATTAWTR
; description rrtTaTTTtrsasykCGwAAttaatg
; statistical_basis 7 sequences
; sites 7
; nb_sites 7
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 13.8963
; information.per.column 0.534474
; max.possible.info.per.col 1.58952
; consensus.strict aatTaTTTtgcagcgCGaAAttaatg
; consensus.strict.rc CATTAATTTCGCGCTGCAAAATAATT
; consensus.IUPAC rrtTaTTTtrsasykCGwAAttaatg
; consensus.IUPAC.rc CATTAATTWCGMRSTSYAAAATAAYY
; consensus.regexp [ag][ag]tTaTTTt[ag][cg]a[cg][ct][gt]CG[at]AAttaatg
; consensus.regexp.rc CATTAATT[AT]CG[AC][AG][CG]T[CG][CT]AAAATAA[CT][CT]
; residues.content.crude.freq a:0.3242|c:0.0989|g:0.1484|t:0.4286
; G+C.content.crude.freq 0.247253
; residues.content.corrected.freq a:0.3200|c:0.1125|g:0.1553|t:0.4121
; G+C.content.corrected.freq 0.267825
; min(P(S|M)) 7.29292e-41
; max(P(S|M)) 1.44184e-05
; proba_range 1.44184e-05
; Wmin -52.4
; Wmax 23
; Wrange 75.4
; logo file:/Mlc.EcolK12_2nt_upstream.26.meme_quality_logo_m1.png
; logo file:/Mlc.EcolK12_2nt_upstream.26.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161014
; Job done 2019-06-03.161015
; Seconds 0.59
; user 0.59
; system 0.05
; cuser 0.45
; csystem 0.05