RegulonDB
LexA matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/LexA/LexA.EcolK12_1nt_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 /LexA.EcolK12_1nt_upstream.22.meme_quality_logo
; Input files
; input /LexA.EcolK12_1nt_upstream.22.meme_quality_matrix.tf
; prior /LexA.EcolK12_1nt_upstream.22.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /LexA.EcolK12_1nt_upstream.22.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 9 20 3 2 3 0 12 10 15 6 16 3 32 6 24 1 40 0 2 20 17 20
C 9 9 36 2 1 1 3 5 1 1 7 6 6 1 11 42 0 0 9 1 5 3
G 5 11 1 2 39 15 11 2 8 0 6 1 3 6 3 1 2 43 5 5 6 6
T 21 4 4 38 1 28 18 27 20 37 15 34 3 31 6 0 2 1 28 18 16 15
//
A 0.2 0.5 0.1 0.1 0.1 0.0 0.3 0.2 0.3 0.1 0.4 0.1 0.7 0.1 0.5 0.0 0.9 0.0 0.1 0.5 0.4 0.5
C 0.2 0.2 0.8 0.0 0.0 0.0 0.1 0.1 0.0 0.0 0.2 0.1 0.1 0.0 0.2 0.9 0.0 0.0 0.2 0.0 0.1 0.1
G 0.1 0.2 0.0 0.0 0.9 0.3 0.2 0.0 0.2 0.0 0.1 0.0 0.1 0.1 0.1 0.0 0.0 1.0 0.1 0.1 0.1 0.1
T 0.5 0.1 0.1 0.9 0.0 0.6 0.4 0.6 0.5 0.8 0.3 0.8 0.1 0.7 0.1 0.0 0.1 0.0 0.6 0.4 0.4 0.3
//
A -0.3 0.4 -1.4 -1.7 -1.4 -3.8 -0.1 -0.2 0.2 -0.7 0.2 -1.4 0.9 -0.7 0.6 -2.3 1.1 -3.8 -1.7 0.4 0.3 0.4
C -0.0 -0.0 1.4 -1.4 -2.0 -2.0 -1.1 -0.6 -2.0 -2.0 -0.3 -0.4 -0.4 -2.0 0.2 1.5 -3.8 -3.8 -0.0 -2.0 -0.6 -1.1
G -0.6 0.2 -2.0 -1.4 1.5 0.5 0.2 -1.4 -0.1 -3.8 -0.4 -2.0 -1.1 -0.4 -1.1 -2.0 -1.4 1.5 -0.6 -0.6 -0.4 -0.4
T 0.5 -1.1 -1.1 1.1 -2.3 0.7 0.3 0.7 0.4 1.0 0.1 0.9 -1.4 0.8 -0.8 -3.8 -1.8 -2.3 0.7 0.3 0.2 0.1
//
A -0.1 0.2 -0.1 -0.1 -0.1 -0.0 -0.0 -0.1 0.1 -0.1 0.1 -0.1 0.6 -0.1 0.3 -0.1 1.0 -0.0 -0.1 0.2 0.1 0.2
C -0.0 -0.0 1.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 0.0 1.4 -0.0 -0.0 -0.0 -0.1 -0.1 -0.1
G -0.1 0.0 -0.1 -0.1 1.3 0.2 0.0 -0.1 -0.0 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 1.5 -0.1 -0.1 -0.1 -0.1
T 0.2 -0.1 -0.1 0.9 -0.1 0.5 0.1 0.4 0.2 0.8 0.0 0.7 -0.1 0.6 -0.1 -0.0 -0.1 -0.1 0.5 0.1 0.1 0.0
//
; Sites 44
>site_0
TACTGTTTTTATATACAGTATA
>site_1
TACTGTTTATTTATACAGTAAA
>site_2
TACTGTTTTTATATACAGTAGT
>site_3
AACTGGTTTTATATACAGTAAA
>site_4
AACTGTTTTTTTATCCAGTATA
>site_5
AACTGTGATTTTATACAGTATA
>site_6
TACTGGTTATTTATACAGGTAA
>site_7
AACTGTATTTATATACAGTTGT
>site_8
CCCTGGGTGTATATACAGTTAT
>site_9
TGCTGTGAGTATATACAGCAAA
>site_10
TGCTGGTTATCTATCCAGTGTA
>site_11
AGCTGTTTATTTATACAGTGAG
>site_12
TACTGTTATTGTGTACAGTATA
>site_13
CCCTGTAATTTTATCCAGTTGA
>site_14
CGCTGGATATCTATCCAGCATT
>site_15
TACTGTATGATTATCCAGTTAG
>site_16
TGCTGTATATTTATTCAGCTTG
>site_17
AGCTGGGTATATATACAGATTT
>site_18
TACTGTATGAGCATACAGTATA
>site_19
TACTGTACGTATCGACAGTTTA
>site_20
TATTGGCTGTTTATACAGTATT
>site_21
TACTGTACATCCATACAGTAAC
>site_22
TCCTGTTAATCCATACAGCAAC
>site_23
TACTGTATATTCATTCAGGTCA
>site_24
CACTGGTAAAGTATACAGTGAT
>site_25
ACCTGTATATATCATCAGTAAA
>site_26
CGCTGGGTTTTTAATCAGTTGC
>site_27
GGCTGTGGTTTTATACAGTCAT
>site_28
TGCTGGTTTTATAACCTGCATG
>site_29
CTCTGGTTTATTGTGCAGTTTA
>site_30
TATAGGATTTTTATACAGTGCA
>site_31
GGCTGCGCTTATCGACAGTTAT
>site_32
TACTGTGAAACGATCCGGTAAG
>site_33
TACTGTGCCATTTTTCAGTTCA
>site_34
GCCTGTTTTTATTTCAGGCAAT
>site_35
CGCTGGCATCAACGCCAGCTTA
>site_36
CTATGTTTATATAACCATCAGT
>site_37
GCCTGGCTTTCAGGGCAGCGTT
>site_38
TTGCATTTATCTAACCAGTTAA
>site_39
GTCTGTTCTTGCCAGCAGATCA
>site_40
CAAGATGAGTGATGACAGTTTT
>site_41
ACACATGGTTATCCACAGGAAT
>site_42
ACTATTATGTATATTCTGGTGT
>site_43
TCTGCGTATTGCAGAGAGGACG
;
; Matrix parameters
; Number of sites 44
; Columns 22
; 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 TRCTGKDTWTWTATACAGTWWW
; AC TRCTGKDTWTWTATACAGTWWW
; id TRCTGKDTWTWTATACAGTWWW
; name TRCTGKDTWTWTATACAGTWWW
; description trCTGkktwTwtatmCAGtwww
; statistical_basis 44 sequences
; sites 44
; nb_sites 44
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 10.1625
; information.per.column 0.461931
; max.possible.info.per.col 1.58873
; consensus.strict taCTGttttTatataCAGtaaa
; consensus.strict.rc TTTACTGTATATAAAAACAGTA
; consensus.IUPAC trCTGkktwTwtatmCAGtwww
; consensus.IUPAC.rc WWWACTGKATAWAWAMMCAGYA
; consensus.regexp t[ag]CTG[gt][gt]t[at]T[at]tat[ac]CAGt[at][at][at]
; consensus.regexp.rc [AT][AT][AT]ACTG[GT]ATA[AT]A[AT]A[AC][AC]CAG[CT]A
; residues.content.crude.freq a:0.2696|c:0.1643|g:0.1870|t:0.3791
; G+C.content.crude.freq 0.35124
; residues.content.corrected.freq a:0.2701|c:0.1652|g:0.1874|t:0.3773
; G+C.content.corrected.freq 0.352584
; min(P(S|M)) 8.48873e-34
; max(P(S|M)) 2.17345e-05
; proba_range 2.17345e-05
; Wmin -43.8
; Wmax 17.6
; Wrange 61.4
; logo file:/LexA.EcolK12_1nt_upstream.22.meme_quality_logo_m1.png
; logo file:/LexA.EcolK12_1nt_upstream.22.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160959
; Job done 2019-06-03.161000
; Seconds 0.58
; user 0.58
; system 0.04
; cuser 0.45
; csystem 0.05