RegulonDB
AraC matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/AraC/AraC.EcolK12_1nt_upstream.20.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 /AraC.EcolK12_1nt_upstream.20.meme_quality_logo
; Input files
; input /AraC.EcolK12_1nt_upstream.20.meme_quality_matrix.tf
; prior /AraC.EcolK12_1nt_upstream.20.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /AraC.EcolK12_1nt_upstream.20.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 4 7 1 11 3 2 6 5 5 9 6 8 6 2 3 2 12 0 11 9
C 6 2 7 0 0 8 5 1 0 0 0 3 3 1 9 12 2 1 1 1
G 1 3 2 2 11 1 3 6 8 1 1 1 5 1 3 0 0 0 2 0
T 4 3 5 2 1 4 1 3 2 5 8 3 1 11 0 1 1 14 1 5
//
A 0.3 0.5 0.1 0.7 0.2 0.1 0.4 0.3 0.3 0.6 0.4 0.5 0.4 0.1 0.2 0.1 0.8 0.0 0.7 0.6
C 0.4 0.1 0.5 0.0 0.0 0.5 0.3 0.1 0.0 0.0 0.0 0.2 0.2 0.1 0.6 0.8 0.1 0.1 0.1 0.1
G 0.1 0.2 0.1 0.1 0.7 0.1 0.2 0.4 0.5 0.1 0.1 0.1 0.3 0.1 0.2 0.0 0.0 0.0 0.1 0.0
T 0.3 0.2 0.3 0.1 0.1 0.3 0.1 0.2 0.1 0.3 0.5 0.2 0.1 0.7 0.0 0.1 0.1 0.9 0.1 0.3
//
A -0.1 0.4 -1.3 0.9 -0.3 -0.7 0.3 0.1 0.1 0.7 0.3 0.6 0.3 -0.7 -0.3 -0.7 1.0 -2.8 0.9 0.7
C 0.6 -0.4 0.8 -2.8 -2.8 0.9 0.4 -1.0 -2.8 -2.8 -2.8 -0.0 -0.0 -1.0 1.0 1.3 -0.4 -1.0 -1.0 -1.0
G -1.0 -0.0 -0.4 -0.4 1.2 -1.0 -0.0 0.6 0.9 -1.0 -1.0 -1.0 0.5 -1.0 -0.0 -2.8 -2.8 -2.8 -0.4 -2.8
T -0.1 -0.4 0.1 -0.7 -1.3 -0.1 -1.3 -0.4 -0.7 0.1 0.6 -0.4 -1.3 0.9 -2.8 -1.3 -1.3 1.1 -1.3 0.1
//
A -0.0 0.2 -0.1 0.6 -0.1 -0.1 0.1 0.0 0.0 0.4 0.1 0.3 0.1 -0.1 -0.1 -0.1 0.7 -0.1 0.6 0.4
C 0.2 -0.1 0.3 -0.0 -0.0 0.5 0.1 -0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1 0.6 1.0 -0.1 -0.1 -0.1 -0.1
G -0.1 -0.0 -0.1 -0.1 0.9 -0.1 -0.0 0.2 0.5 -0.1 -0.1 -0.1 0.2 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0
T -0.0 -0.1 0.0 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 0.0 0.3 -0.1 -0.1 0.6 -0.1 -0.1 -0.1 1.0 -0.1 0.0
//
; Sites 15
>site_0
CACAGCAGATTAATCCATAA
>site_1
CGCAGCAATTTAATCCATAT
>site_2
TACAGTGAGAACGTGCATAA
>site_3
CATAGCATTTTTATCCATAA
>site_4
CACGGCAGAAAAGTCCACAT
>site_5
TTTAGCGGGAAAAGACATAA
>site_6
TTCAGCAGGATAATGAATAC
>site_7
AGCAGTGTGAAATAACATAA
>site_8
AAGAAACCAATTGTCCATAT
>site_9
CGTAACAAAAGTGTCTATAA
>site_10
ATTAGCCTGGAAATCCTTGT
>site_11
TCAGGTCGGAAACAGCATAA
>site_12
GATTAGCGGATCCTACCTGA
>site_13
AAGAGATAATTCGCCCCTCT
>site_14
CCCTTTCAGTTGCTCAATTA
;
; Matrix parameters
; Number of sites 15
; Columns 20
; 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 HAYAGYVDRWWAVTCCATAW
; AC HAYAGYVDRWWAVTCCATAW
; id HAYAGYVDRWWAVTCCATAW
; name HAYAGYVDRWWAVTCCATAW
; description cayaGcmrrwwartCCaTaw
; statistical_basis 15 sequences
; sites 15
; nb_sites 15
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 6.99812
; information.per.column 0.349906
; max.possible.info.per.col 1.58873
; consensus.strict cacaGccggatagtCCaTaa
; consensus.strict.rc TTATGGACTATCCGGCTGTG
; consensus.IUPAC cayaGcmrrwwartCCaTaw
; consensus.IUPAC.rc WTATGGAYTWWYYKGCTRTG
; consensus.regexp ca[ct]aGc[ac][ag][ag][at][at]a[ag]tCCaTa[at]
; consensus.regexp.rc [AT]TATGGA[CT]T[AT][AT][CT][CT][GT]GCT[AG]TG
; residues.content.crude.freq a:0.3733|c:0.2067|g:0.1700|t:0.2500
; G+C.content.crude.freq 0.376667
; residues.content.corrected.freq a:0.3682|c:0.2067|g:0.1721|t:0.2530
; G+C.content.corrected.freq 0.378859
; min(P(S|M)) 2.42189e-30
; max(P(S|M)) 8.44392e-06
; proba_range 8.44392e-06
; Wmin -38.4
; Wmax 16.1
; Wrange 54.5
; logo file:/AraC.EcolK12_1nt_upstream.20.meme_quality_logo_m1.png
; logo file:/AraC.EcolK12_1nt_upstream.20.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.59
; user 0.59
; system 0.06
; cuser 0.43
; csystem 0.05