RegulonDB
ArgR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/ArgR/ArgR.EcolK12_1nt_upstream.21.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 /ArgR.EcolK12_1nt_upstream.21.meme_quality_logo
; Input files
; input /ArgR.EcolK12_1nt_upstream.21.meme_quality_matrix.tf
; prior /ArgR.EcolK12_1nt_upstream.21.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /ArgR.EcolK12_1nt_upstream.21.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 11 12 13 13 11 0 1 10 23 2 17 22 17 17 25 2 2 0 17 6 6
C 6 3 1 1 2 0 0 16 0 1 1 1 1 1 1 2 3 25 2 7 3
G 1 1 4 0 6 0 30 3 2 0 8 0 2 0 1 3 4 3 6 7 2
T 13 15 13 17 12 31 0 2 6 28 5 8 11 13 4 24 22 3 6 11 20
//
A 0.4 0.4 0.4 0.4 0.4 0.0 0.0 0.3 0.7 0.1 0.5 0.7 0.5 0.5 0.8 0.1 0.1 0.0 0.5 0.2 0.2
C 0.2 0.1 0.0 0.0 0.1 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.1 0.8 0.1 0.2 0.1
G 0.0 0.0 0.1 0.0 0.2 0.0 0.9 0.1 0.1 0.0 0.3 0.0 0.1 0.0 0.0 0.1 0.1 0.1 0.2 0.2 0.1
T 0.4 0.5 0.4 0.5 0.4 1.0 0.0 0.1 0.2 0.9 0.2 0.3 0.4 0.4 0.1 0.8 0.7 0.1 0.2 0.4 0.6
//
A 0.2 0.3 0.4 0.4 0.2 -3.5 -2.0 0.1 0.9 -1.4 0.6 0.9 0.6 0.6 1.0 -1.4 -1.4 -3.5 0.6 -0.4 -0.4
C -0.1 -0.7 -1.7 -1.7 -1.1 -3.5 -3.5 0.9 -3.5 -1.7 -1.7 -1.7 -1.7 -1.7 -1.7 -1.1 -0.7 1.3 -1.1 0.1 -0.7
G -1.7 -1.7 -0.4 -3.5 -0.1 -3.5 1.5 -0.7 -1.1 -3.5 0.2 -3.5 -1.1 -3.5 -1.7 -0.7 -0.4 -0.7 -0.1 0.1 -1.1
T 0.3 0.5 0.3 0.6 0.3 1.2 -3.5 -1.4 -0.4 1.1 -0.6 -0.1 0.2 0.3 -0.8 0.9 0.9 -1.1 -0.4 0.2 0.8
//
A 0.1 0.1 0.1 0.1 0.1 -0.0 -0.1 0.0 0.7 -0.1 0.3 0.6 0.3 0.3 0.8 -0.1 -0.1 -0.0 0.3 -0.1 -0.1
C -0.0 -0.1 -0.1 -0.1 -0.1 -0.0 -0.0 0.5 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 1.1 -0.1 0.0 -0.1
G -0.1 -0.1 -0.1 -0.0 -0.0 -0.0 1.4 -0.1 -0.1 -0.0 0.1 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.0 0.0 -0.1
T 0.1 0.2 0.1 0.3 0.1 1.2 -0.0 -0.1 -0.1 1.0 -0.1 -0.0 0.1 0.1 -0.1 0.7 0.6 -0.1 -0.1 0.1 0.5
//
; Sites 31
>site_0
TATTTTGCATAAAAATTCAGT
>site_1
TTTATTGCATATAAATTCACT
>site_2
AATATTGCATAATTATTCTGT
>site_3
CTGTTTGCATAAAAATTCATC
>site_4
CTTATTGAATTAAAATTCACT
>site_5
TTATATGGATGATTATTCATT
>site_6
TTATTTGCATATTAATTCACA
>site_7
AAATATGCATAAAAAATCACT
>site_8
ATTTATGAATAAAAATACACT
>site_9
TAAATTGAATTTTAATTCATT
>site_10
TCATGTGAATGAATATCCAGT
>site_11
AATTTTGATTGATTATGCAGT
>site_12
TTATATGTGTAATTATTCATT
>site_13
GATTATGCATGAAATTTCGGT
>site_14
AAAAATGCTTAAGTATGCATT
>site_15
TAAAGTGAGTGAATATTCTCT
>site_16
AATACTGCATGAATATTGATA
>site_17
CTCTTTGCATGATTATTCGAA
>site_18
ATTAGTGTATTTTTATTCTGT
>site_19
TTTTGTGGTTATAATTTCACA
>site_20
CCTTATGCATAACATTTCCTT
>site_21
ATGATTAAATGAAAACTCATT
>site_22
TTTAATGAAAAATAATACGTC
>site_23
CTGTATGCACAATAATGTTGT
>site_24
ATTTCTGCTTTAAAAGTTAAA
>site_25
CCATATGCATTTAAAGTGCAT
>site_26
TAAAGTGAATACGTTTGCGAT
>site_27
TTAATTGCAACTTTACTCGTC
>site_28
AAACATGATTAAATAATTTAA
>site_29
TGGTTTGGTTATAACTCCTTG
>site_30
AAAAGTGCATAAACGGCGGAG
;
; Matrix parameters
; Number of sites 31
; Columns 21
; 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 WWWWDTGMATAAWWATTCANT
; AC WWWWDTGMATAAWWATTCANT
; id WWWWDTGMATAAWWATTCANT
; name WWWWDTGMATAAWWATTCANT
; description wwwwwTGmaTrawwattCabt
; statistical_basis 31 sequences
; sites 31
; nb_sites 31
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 8.96129
; information.per.column 0.426728
; max.possible.info.per.col 1.58873
; consensus.strict ttattTGcaTaaaaattCatt
; consensus.strict.rc AATGAATTTTTATGCAAATAA
; consensus.IUPAC wwwwwTGmaTrawwattCabt
; consensus.IUPAC.rc AVTGAATWWTYATKCAWWWWW
; consensus.regexp [at][at][at][at][at]TG[ac]aT[ag]a[at][at]attCa[cgt]t
; consensus.regexp.rc A[ACG]TGAAT[AT][AT]T[CT]AT[GT]CA[AT][AT][AT][AT][AT]
; residues.content.crude.freq a:0.3487|c:0.1183|g:0.1275|t:0.4055
; G+C.content.crude.freq 0.245776
; residues.content.corrected.freq a:0.3469|c:0.1211|g:0.1299|t:0.4021
; G+C.content.corrected.freq 0.250962
; min(P(S|M)) 2.6472e-34
; max(P(S|M)) 2.26012e-05
; proba_range 2.26012e-05
; Wmin -45.9
; Wmax 16.1
; Wrange 62
; logo file:/ArgR.EcolK12_1nt_upstream.21.meme_quality_logo_m1.png
; logo file:/ArgR.EcolK12_1nt_upstream.21.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 0.46
; csystem 0.05