RegulonDB
Lrp matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/Lrp/Lrp.EcolK12_1nt_upstream.13.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 /Lrp.EcolK12_1nt_upstream.13.meme_quality_logo
; Input files
; input /Lrp.EcolK12_1nt_upstream.13.meme_quality_matrix.tf
; prior /Lrp.EcolK12_1nt_upstream.13.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /Lrp.EcolK12_1nt_upstream.13.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 12 28 35 4 26 13 13 41 11 15 13 0 1
C 8 17 0 12 5 1 7 8 9 25 49 0 0
G 36 16 13 8 8 6 6 5 7 10 4 15 46
T 24 19 32 56 41 60 54 26 53 30 14 65 33
//
A 0.2 0.3 0.4 0.1 0.3 0.2 0.2 0.5 0.1 0.2 0.2 0.0 0.0
C 0.1 0.2 0.0 0.2 0.1 0.0 0.1 0.1 0.1 0.3 0.6 0.0 0.0
G 0.4 0.2 0.2 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.6
T 0.3 0.2 0.4 0.7 0.5 0.7 0.7 0.3 0.7 0.4 0.2 0.8 0.4
//
A -0.7 0.2 0.4 -1.7 0.1 -0.6 -0.6 0.6 -0.7 -0.4 -0.6 -4.4 -2.9
C -0.7 0.0 -4.4 -0.3 -1.2 -2.6 -0.8 -0.7 -0.6 0.4 1.1 -4.4 -4.4
G 0.8 -0.0 -0.2 -0.7 -0.7 -1.0 -1.0 -1.2 -0.8 -0.5 -1.4 -0.1 1.0
T 0.0 -0.2 0.3 0.8 0.5 0.9 0.8 0.1 0.8 0.2 -0.5 1.0 0.3
//
A -0.1 0.1 0.2 -0.1 0.0 -0.1 -0.1 0.3 -0.1 -0.1 -0.1 -0.0 -0.0
C -0.1 0.0 -0.0 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 0.1 0.7 -0.0 -0.0
G 0.4 -0.0 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 0.6
T 0.0 -0.1 0.1 0.6 0.3 0.7 0.5 0.0 0.5 0.1 -0.1 0.8 0.1
//
; Sites 80
>site_0
GAATTTTATTCTG
>site_1
GCATTTTATACTG
>site_2
GAATTTTATGCTG
>site_3
GAATTTTTTTCTT
>site_4
GGATTTTATTCGG
>site_5
GATTATTATTCTT
>site_6
TATTTTTATTCTT
>site_7
TGTTTTTTTTCTT
>site_8
GGATTTTATCTTT
>site_9
GAATTTTGTGCTG
>site_10
ATTTTTTATTCTT
>site_11
GATGTTTTTACTG
>site_12
CGTCTTTATCCTG
>site_13
TGATTTTCTCCTT
>site_14
GTTATTTATCCTG
>site_15
TTTCATTATTCTG
>site_16
GGATTTTATCGTT
>site_17
TTTTTTTACCCTT
>site_18
GAACGTTATCCGG
>site_19
TAATTTTTCTCTT
>site_20
TAACATTATCCGG
>site_21
GCATTTATTTTTG
>site_22
GAGTATTATCTGG
>site_23
GATGTTTATATTG
>site_24
TTGGATTATTCTG
>site_25
GCATATTCACCTT
>site_26
CCTGTTTATTCTT
>site_27
AAATAATTTTCTG
>site_28
AAATAATTTTCTG
>site_29
CTGGTTTATTCTG
>site_30
TGAAATTATTCTG
>site_31
AAGTTTAATTCTT
>site_32
TCTTATTTTTATT
>site_33
GTTTATGTCTCTG
>site_34
TAATATTCTATTG
>site_35
GATTTTGATATTT
>site_36
GCATTAATTCTTG
>site_37
GGGTTTTTGTTTT
>site_38
GCGTATATCGCTG
>site_39
GTACTTTAACTTT
>site_40
AGTTGTCATACTG
>site_41
ATATTTTCAACTG
>site_42
TCTTATTAGTTTT
>site_43
TTAGTATCTCCTG
>site_44
TAATATTAATTGG
>site_45
TGGTATTTACATG
>site_46
TGTTATATGCCTT
>site_47
AATTTATTAACTG
>site_48
GCATCAGATACTG
>site_49
GATTTTTCAATTT
>site_50
CTATTTCAACCGG
>site_51
TCACATCTCCCTG
>site_52
TATTTATTACCGT
>site_53
TCATTGTTGTCGG
>site_54
GGTTATAACCTGG
>site_55
GGAAATTTTTATT
>site_56
TAATTGAATCATT
>site_57
TATGTTTTTAAGG
>site_58
AGTTTTCATAATT
>site_59
GCGCATAACCATG
>site_60
TTTCATGCTACTG
>site_61
CTTTAATTATCTT
>site_62
ACGTTTGTTGTTG
>site_63
GATTGATAGCAGG
>site_64
CAGTCAATTCCTG
>site_65
GATAATAAATCGG
>site_66
CTTCCTCATTCTT
>site_67
CATTTTGATGGTT
>site_68
GTGTAACTTGATG
>site_69
ATATTGTCTTATT
>site_70
TAGTGGCACTCTG
>site_71
TTATTTAGTCAGT
>site_72
ATTCGTTATTGTT
>site_73
GCTCCGTTTCATT
>site_74
GCATGTTGTACTA
>site_75
GCTTGAAATGAGG
>site_76
GGACCTTTCGGTG
>site_77
GTGTGGTAGGCGT
>site_78
GGAGAATGGACTT
>site_79
ACATTCAGTGCTG
;
; Matrix parameters
; Number of sites 80
; Columns 13
; 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 KNWTWTTWTHCTK
; AC KNWTWTTWTHCTK
; id KNWTWTTWTHCTK
; name KNWTWTTWTHCTK
; description kmwtwttwtyCtK
; statistical_basis 80 sequences
; sites 80
; nb_sites 80
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 4.09137
; information.per.column 0.314721
; max.possible.info.per.col 1.58873
; consensus.strict gaattttatcCtG
; consensus.strict.rc CAGGATAAAATTC
; consensus.IUPAC kmwtwttwtyCtK
; consensus.IUPAC.rc MAGRAWAAWAWKM
; consensus.regexp [gt][ac][at]t[at]tt[at]t[ct]Ct[GT]
; consensus.regexp.rc [AC]AG[AG]A[AT]AA[AT]A[AT][GT][AC]
; residues.content.crude.freq a:0.2038|c:0.1356|g:0.1731|t:0.4875
; G+C.content.crude.freq 0.308654
; residues.content.corrected.freq a:0.2049|c:0.1365|g:0.1735|t:0.4852
; G+C.content.corrected.freq 0.309927
; min(P(S|M)) 4.9562e-20
; max(P(S|M)) 0.000421525
; proba_range 0.000421525
; Wmin -24.5
; Wmax 9.4
; Wrange 33.9
; logo file:/Lrp.EcolK12_1nt_upstream.13.meme_quality_logo_m1.png
; logo file:/Lrp.EcolK12_1nt_upstream.13.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161014
; Job done 2019-06-03.161015
; Seconds 0.54
; user 0.54
; system 0.06
; cuser 0.39
; csystem 0.05