RegulonDB
Fur matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/Fur/Fur.EcolK12_2nt_upstream.22.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 /Fur.EcolK12_2nt_upstream.22.meme_quality_logo
; Input files
; input /Fur.EcolK12_2nt_upstream.22.meme_quality_matrix.tf
; prior /Fur.EcolK12_2nt_upstream.22.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /Fur.EcolK12_2nt_upstream.22.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 9 14 39 12 40 40 2 12 32 4 9 25 2 6 42 7 7 22 8 12 38 14
C 7 1 3 2 0 2 8 11 6 1 1 12 6 33 1 1 1 4 12 19 3 1
G 2 31 4 7 3 6 0 20 6 1 0 3 4 5 3 3 0 3 10 4 7 1
T 30 2 2 27 5 0 38 5 4 42 38 8 36 4 2 37 40 19 18 13 0 32
//
A 0.2 0.3 0.8 0.3 0.8 0.8 0.0 0.3 0.7 0.1 0.2 0.5 0.0 0.1 0.9 0.1 0.1 0.5 0.2 0.3 0.8 0.3
C 0.1 0.0 0.1 0.0 0.0 0.0 0.2 0.2 0.1 0.0 0.0 0.2 0.1 0.7 0.0 0.0 0.0 0.1 0.2 0.4 0.1 0.0
G 0.0 0.6 0.1 0.1 0.1 0.1 0.0 0.4 0.1 0.0 0.0 0.1 0.1 0.1 0.1 0.1 0.0 0.1 0.2 0.1 0.1 0.0
T 0.6 0.0 0.0 0.6 0.1 0.0 0.8 0.1 0.1 0.9 0.8 0.2 0.7 0.1 0.0 0.8 0.8 0.4 0.4 0.3 0.0 0.7
//
A -0.4 0.0 1.0 -0.1 1.0 1.0 -1.8 -0.1 0.8 -1.2 -0.4 0.6 -1.8 -0.8 1.1 -0.7 -0.7 0.4 -0.5 -0.1 1.0 0.0
C -0.3 -2.1 -1.2 -1.5 -3.9 -1.5 -0.2 0.1 -0.5 -2.1 -2.1 0.2 -0.5 1.2 -2.1 -2.1 -2.1 -0.9 0.2 0.6 -1.2 -2.1
G -1.5 1.1 -0.9 -0.3 -1.1 -0.5 -3.9 0.7 -0.5 -2.1 -3.9 -1.1 -0.9 -0.7 -1.1 -1.1 -3.9 -1.1 0.0 -0.9 -0.3 -2.1
T 0.7 -1.8 -1.8 0.6 -1.0 -3.9 1.0 -1.0 -1.2 1.1 1.0 -0.6 0.9 -1.2 -1.8 0.9 1.0 0.3 0.2 -0.1 -3.9 0.8
//
A -0.1 0.0 0.8 -0.0 0.9 0.9 -0.1 -0.0 0.5 -0.1 -0.1 0.3 -0.1 -0.1 0.9 -0.1 -0.1 0.2 -0.1 -0.0 0.8 0.0
C -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0 0.0 -0.1 -0.1 -0.1 0.0 -0.1 0.8 -0.1 -0.1 -0.1 -0.1 0.0 0.2 -0.1 -0.1
G -0.1 0.7 -0.1 -0.0 -0.1 -0.1 -0.0 0.3 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 0.0 -0.1 -0.0 -0.1
T 0.5 -0.1 -0.1 0.4 -0.1 -0.0 0.8 -0.1 -0.1 0.9 0.8 -0.1 0.7 -0.1 -0.1 0.7 0.8 0.1 0.1 -0.0 -0.0 0.5
//
; Sites 48
>site_0
TAATAATGATTATCATTTATAT
>site_1
TGAGAATGGTTATCATTACAAT
>site_2
CAATAATGCTTCTCATTTTCAT
>site_3
TGATAACGATTTTCATTTGGAT
>site_4
TGATAATGATTATCATCTACAT
>site_5
TGATAGTCGTTCTCATTACTAT
>site_6
TGATAATGATAACCAATATCAT
>site_7
TGATAATCATTATCACTAACAT
>site_8
TGATAATTTTTATCATTTGCAA
>site_9
TGGAAATCATTTTCATTTTTAT
>site_10
TGATAATGCTTATCAAAATTAT
>site_11
TGAAAATGATTATCAATGCCGT
>site_12
CGAGAATGATTATCAAATTCAT
>site_13
TGTTAATTATTCTCATTACCAA
>site_14
TAGAAACCATTCTCATTATCAT
>site_15
CGATAATTAATTTCATTATCAT
>site_16
TAACAATCATTATCATTTGCGA
>site_17
TAATAATCATTCTCGTTTACGT
>site_18
AAAAAATAATTAGCATTAGAAT
>site_19
AGACAATAATAATCATTCTCAT
>site_20
TAAAAACACTTATCATTATAAA
>site_21
TGATAACTATTTGCATTTGCAA
>site_22
TGAGAATTATTATCATTAAAAG
>site_23
TGATAATAATTCTTAGTATTAA
>site_24
TGAAAGTGATAATAATTTTGAT
>site_25
CGATAACAATTATCAATCCAAA
>site_26
AACAAATAATTATCATTAGAGT
>site_27
GGAAAATAATTCTTATTTCGAT
>site_28
AGATAATGCGTATCATTATAGA
>site_29
TGAATATGATTGCTATTTGCAT
>site_30
TGCGTATATTTCTCATTTGCAT
>site_31
TGGAAATAATTCACATTAAAAA
>site_32
TGATAATATTATTGATAACTAT
>site_33
TGATAATGCATATAATTTTAAC
>site_34
TAATTATCGTTATCGATCTTAT
>site_35
CAATAAAAATAATCAGTAATAT
>site_36
TTGAAGTCATAATCATTTCAGT
>site_37
CGATAATGCAAACGATAACAAT
>site_38
ACAAAATCATTACAATTAACCT
>site_39
TGCGAATAATTTTGTTTGTAAA
>site_40
TGATAAAGGCTTTAATAATGAT
>site_41
TTATTCCCATTCGTATTTTTAA
>site_42
AATTGATGTATCTCAAATGCAT
>site_43
AAATAGCGGTAATGCGTTTTAT
>site_44
AAATTGTCATTCCATTTACTGA
>site_45
CGAGGCCGATTGCCGTTGCTAA
>site_46
AAATAGTGGTCGAAATTACCCT
>site_47
GGAGGATGATATGGATACGTCA
;
; Matrix parameters
; Number of sites 48
; Columns 22
; 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 TGATAATVATTATCATTWBHAT
; AC TGATAATVATTATCATTWBHAT
; id TGATAATVATTATCATTWBHAT
; name TGATAATVATTATCATTWBHAT
; description tRAtAAtsaTtmtCAtTwbcaw
; statistical_basis 48 sequences
; sites 48
; nb_sites 48
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 9.76792
; information.per.column 0.443996
; max.possible.info.per.col 1.58952
; consensus.strict tGAtAAtgaTtatCAtTatcat
; consensus.strict.rc ATGATAATGATAATCATTATCA
; consensus.IUPAC tRAtAAtsaTtmtCAtTwbcaw
; consensus.IUPAC.rc WTGVWAATGAKAATSATTATYA
; consensus.regexp t[AG]AtAAt[cg]aTt[ac]tCAtT[at][cgt]ca[at]
; consensus.regexp.rc [AT]TG[ACG][AT]AATGA[GT]AAT[CG]ATTAT[CT]A
; residues.content.crude.freq a:0.3750|c:0.1278|g:0.1165|t:0.3807
; G+C.content.crude.freq 0.244318
; residues.content.corrected.freq a:0.3733|c:0.1295|g:0.1183|t:0.3790
; G+C.content.corrected.freq 0.247737
; min(P(S|M)) 2.3317e-35
; max(P(S|M)) 8.18116e-05
; proba_range 8.18116e-05
; Wmin -47.9
; Wmax 19
; Wrange 66.9
; logo file:/Fur.EcolK12_2nt_upstream.22.meme_quality_logo_m1.png
; logo file:/Fur.EcolK12_2nt_upstream.22.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.6
; user 0.6
; system 0.06
; cuser 0.45
; csystem 0.04