RegulonDB
FNR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/FNR/FNR.EcolK12_1nt_upstream.14.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 /FNR.EcolK12_1nt_upstream.14.meme_quality_logo
; Input files
; input /FNR.EcolK12_1nt_upstream.14.meme_quality_matrix.tf
; prior /FNR.EcolK12_1nt_upstream.14.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /FNR.EcolK12_1nt_upstream.14.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 2 10 77 0 29 17 29 38 57 12 2 66 49
C 1 0 2 0 17 15 8 18 5 16 4 63 6 14
G 6 1 76 2 0 22 9 14 26 2 17 11 8 8
T 81 85 0 9 71 22 54 27 19 13 55 12 8 17
//
A 0.0 0.0 0.1 0.9 0.0 0.3 0.2 0.3 0.4 0.6 0.1 0.0 0.7 0.6
C 0.0 0.0 0.0 0.0 0.2 0.2 0.1 0.2 0.1 0.2 0.0 0.7 0.1 0.2
G 0.1 0.0 0.9 0.0 0.0 0.2 0.1 0.2 0.3 0.0 0.2 0.1 0.1 0.1
T 0.9 1.0 0.0 0.1 0.8 0.3 0.6 0.3 0.2 0.1 0.6 0.1 0.1 0.2
//
A -4.5 -2.4 -0.9 1.1 -4.5 0.1 -0.4 0.1 0.4 0.8 -0.7 -2.4 0.9 0.6
C -2.7 -4.5 -2.1 -4.5 -0.1 -0.2 -0.8 -0.0 -1.3 -0.1 -1.5 1.2 -1.1 -0.3
G -1.1 -2.7 1.4 -2.1 -4.5 0.2 -0.7 -0.2 0.4 -2.1 -0.1 -0.5 -0.8 -0.8
T 1.1 1.2 -4.5 -1.0 1.0 -0.2 0.7 0.0 -0.3 -0.7 0.7 -0.8 -1.2 -0.4
//
A -0.0 -0.1 -0.1 0.9 -0.0 0.0 -0.1 0.0 0.2 0.5 -0.1 -0.1 0.7 0.4
C -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.1 -0.0 -0.1 -0.0 -0.1 0.9 -0.1 -0.0
G -0.1 -0.0 1.2 -0.1 -0.0 0.0 -0.1 -0.0 0.1 -0.1 -0.0 -0.1 -0.1 -0.1
T 1.0 1.1 -0.0 -0.1 0.8 -0.0 0.4 0.0 -0.1 -0.1 0.5 -0.1 -0.1 -0.1
//
; Sites 88
>site_0
TTGATGTAAATCAA
>site_1
TTGATGTTAATCAA
>site_2
TTGATTTAAATCAA
>site_3
TTGATATTTATCAA
>site_4
TTGATATATATCAA
>site_5
TTGATGTAGCTCAA
>site_6
TTGATATAGATCAT
>site_7
TTGATTTAAATCAC
>site_8
TTGATGTGGCTCAA
>site_9
TTGATAACGATCAA
>site_10
TTGATAACGATCAA
>site_11
TTGATGTAAAACAA
>site_12
TTGATTTGGATCAC
>site_13
TTGATGTATCTCAA
>site_14
TTGATAGGAATCAA
>site_15
TTGACATATATCAA
>site_16
TTGATATTTATCAT
>site_17
TTGATATTTATCAT
>site_18
TTGATTTAGCGCAA
>site_19
TTGATGTTAATTAA
>site_20
TTGATTTCGCGCAA
>site_21
TTGATCTTAATTAA
>site_22
TTGATATGGATTAA
>site_23
TTGACTTCGCTCAA
>site_24
TTGACGTTAAACAA
>site_25
TTGTTCTCGATCAA
>site_26
TTGATGATATTCAA
>site_27
TTGATCTGGATTAA
>site_28
TTGATTGAAATCAT
>site_29
TTGATATACATCAT
>site_30
TTGATTTAGATCGC
>site_31
TTGATGCAAAGCAC
>site_32
TTGACAAATATCAA
>site_33
TTGATCTTACGCAT
>site_34
TTGATACCGAACAA
>site_35
TTGATTTCGCGCAT
>site_36
TTGATTTATTTCAC
>site_37
TTGTCTTTAATCAA
>site_38
TTGATTTCTCACAA
>site_39
TTGACAAAAATCAG
>site_40
TTGATGGTAAGGAA
>site_41
TTGACCTGTATCAG
>site_42
TTAATATTTAGCAA
>site_43
TTGACCTACCTCAA
>site_44
TTGATATATAACTA
>site_45
TTGACTTTAGTCAA
>site_46
TTGATGACGACCAT
>site_47
TTGATGCTAATCCT
>site_48
TTAATAGTAAGCAA
>site_49
TTGATCCAGAACAG
>site_50
TTAATTTTGATTAA
>site_51
GTGATACCAATCAC
>site_52
TTGATCTACATCTC
>site_53
TTAACCTGGCTCAA
>site_54
TTGACAGTTAGCAT
>site_55
TTGATAACGAGCGG
>site_56
TTGTTAAGATTCAA
>site_57
TTGTTTTATTTCAC
>site_58
TTGATAACAACCCA
>site_59
TGGATGTTAAACAA
>site_60
TTGATGCGGAACGC
>site_61
TTAACGTTCAGCAA
>site_62
CTGATAATAAGCAA
>site_63
GTAATCTGGATCAC
>site_64
TTGATCTGGTTTGC
>site_65
TTGATCTCACCCGG
>site_66
GAGATGTAAAGCAA
>site_67
TTGTTGATATTTAA
>site_68
TTGTTATCTATGTA
>site_69
TTGACAGTGAGGCA
>site_70
TTGATGTGGTTTTT
>site_71
TTGATTTTATTTTG
>site_72
TTGGCAATTATCAC
>site_73
GTGATTTCATGCGT
>site_74
TTGATCGAACAGCA
>site_75
TTCATACAAAACAG
>site_76
TTGATAATCATTTT
>site_77
TTGATCCTGCTACA
>site_78
TTAATTGCAATGGT
>site_79
GTGTTTTCATGGAA
>site_80
TTGATTGGTGTGAG
>site_81
TTGACGAGATCGAT
>site_82
TTCTTATAAATGCA
>site_83
TTAGTCAAAATGAT
>site_84
TAAATTTATTTGAA
>site_85
TTGATGACATAAGC
>site_86
GTGACGATACATTC
>site_87
TTATCTTATCGTTT
;
; Matrix parameters
; Number of sites 88
; Columns 14
; 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 TTGATNTHDATCAA
; AC TTGATNTHDATCAA
; id TTGATNTHDATCAA
; name TTGATNTHDATCAA
; description TTGAtrtwratCaa
; statistical_basis 88 sequences
; sites 88
; nb_sites 88
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 6.72032
; information.per.column 0.480023
; max.possible.info.per.col 1.58873
; consensus.strict TTGAtgtaaatCaa
; consensus.strict.rc TTGATTTACATCAA
; consensus.IUPAC TTGAtrtwratCaa
; consensus.IUPAC.rc TTGATYWAYATCAA
; consensus.regexp TTGAt[ag]t[at][ag]atCaa
; consensus.regexp.rc TTGAT[CT][AT]A[CT]ATCAA
; residues.content.crude.freq a:0.3149|c:0.1372|g:0.1640|t:0.3839
; G+C.content.crude.freq 0.301136
; residues.content.corrected.freq a:0.3147|c:0.1380|g:0.1644|t:0.3830
; G+C.content.corrected.freq 0.302379
; min(P(S|M)) 3.88547e-24
; max(P(S|M)) 0.00173721
; proba_range 0.00173721
; Wmin -33
; Wmax 11.6
; Wrange 44.6
; logo file:/FNR.EcolK12_1nt_upstream.14.meme_quality_logo_m1.png
; logo file:/FNR.EcolK12_1nt_upstream.14.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 0.42
; csystem 0.04