RegulonDB
PurR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/PurR/PurR.EcolK12_1nt_upstream.17.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 /PurR.EcolK12_1nt_upstream.17.meme_quality_logo
; Input files
; input /PurR.EcolK12_1nt_upstream.17.meme_quality_matrix.tf
; prior /PurR.EcolK12_1nt_upstream.17.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /PurR.EcolK12_1nt_upstream.17.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 15 3 0 1 22 22 14 0 0 2 0 0 5 0 2 2 1
C 0 15 1 20 0 0 2 22 0 0 0 1 1 21 8 2 3
G 6 2 21 1 0 0 1 0 22 5 1 1 2 0 6 1 4
T 1 2 0 0 0 0 5 0 0 15 21 20 14 1 6 17 14
//
A 0.7 0.1 0.0 0.1 1.0 1.0 0.6 0.0 0.0 0.1 0.0 0.0 0.2 0.0 0.1 0.1 0.1
C 0.0 0.7 0.1 0.9 0.0 0.0 0.1 1.0 0.0 0.0 0.0 0.1 0.1 0.9 0.4 0.1 0.1
G 0.3 0.1 0.9 0.1 0.0 0.0 0.1 0.0 1.0 0.2 0.1 0.1 0.1 0.0 0.3 0.1 0.2
T 0.1 0.1 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.7 0.9 0.9 0.6 0.1 0.3 0.8 0.6
//
A 0.8 -0.7 -3.1 -1.6 1.2 1.2 0.8 -3.1 -3.1 -1.1 -3.1 -3.1 -0.2 -3.1 -1.1 -1.1 -1.6
C -3.1 1.2 -1.4 1.4 -3.1 -3.1 -0.8 1.5 -3.1 -3.1 -3.1 -1.4 -1.4 1.5 0.5 -0.8 -0.4
G 0.3 -0.8 1.5 -1.4 -3.1 -3.1 -1.4 -3.1 1.6 0.1 -1.4 -1.4 -0.8 -3.1 0.3 -1.4 -0.1
T -1.7 -1.1 -3.1 -3.1 -3.1 -3.1 -0.3 -3.1 -3.1 0.8 1.1 1.1 0.7 -1.7 -0.1 0.9 0.7
//
A 0.5 -0.1 -0.0 -0.1 1.2 1.2 0.5 -0.0 -0.0 -0.1 -0.0 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1
C -0.0 0.8 -0.1 1.3 -0.0 -0.0 -0.1 1.5 -0.0 -0.0 -0.0 -0.1 -0.1 1.4 0.2 -0.1 -0.1
G 0.1 -0.1 1.4 -0.1 -0.0 -0.0 -0.1 -0.0 1.5 0.0 -0.1 -0.1 -0.1 -0.0 0.1 -0.1 -0.0
T -0.1 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 0.5 1.1 1.0 0.5 -0.1 -0.0 0.7 0.5
//
; Sites 22
>site_0
ACGCAAACGTTTTCGTT
>site_1
ACGCAAACGTTTTCTTT
>site_2
GCGCAAACGTTTTCGTT
>site_3
ACGCAACCGTTTTCCTT
>site_4
ACGCAAACGGTTTCGTC
>site_5
ACGCAATCGGTTACCTT
>site_6
ACGCAAACGATTACCTT
>site_7
AGGCAAACGTTTACCTT
>site_8
GCGCAACCGGTTTCTTT
>site_9
GCGGAAACGTTTTCCTT
>site_10
AAGCAATCGTTTTCGTG
>site_11
ACGCAATCGTTCTCTTT
>site_12
TCGCAAACGTTTGCTTT
>site_13
ACGCAAACGTTTTCCGA
>site_14
GCGAAAACGTTTTCTTG
>site_15
ACGCAAACGTGTGCGTC
>site_16
GCGCAAGCGTTTTCCAG
>site_17
AGCCAATCGTTTTCCTC
>site_18
ATGCAATCGGTTACGCT
>site_19
GAGCAAACGTTTCCACT
>site_20
ATGCAAACGATTTCAAG
>site_21
AAGCAAACGGTGATTTT
;
; Matrix parameters
; Number of sites 22
; Columns 17
; 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 ACGCAAACGTTTTCBTT
; AC ACGCAAACGTTTTCBTT
; id ACGCAAACGTTTTCBTT
; name ACGCAAACGTTTTCBTT
; description rCGCAAaCGkTTtCstt
; statistical_basis 22 sequences
; sites 22
; nb_sites 22
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 12.9229
; information.per.column 0.760173
; max.possible.info.per.col 1.58873
; consensus.strict aCGCAAaCGtTTtCctt
; consensus.strict.rc AAGGAAAACGTTTGCGT
; consensus.IUPAC rCGCAAaCGkTTtCstt
; consensus.IUPAC.rc AASGAAAMCGTTTGCGY
; consensus.regexp [ag]CGCAAaCG[gt]TTtC[cg]tt
; consensus.regexp.rc AA[CG]GAAA[AC]CGTTTGCG[CT]
; residues.content.crude.freq a:0.2380|c:0.2567|g:0.1952|t:0.3102
; G+C.content.crude.freq 0.451872
; residues.content.corrected.freq a:0.2403|c:0.2545|g:0.1956|t:0.3096
; G+C.content.corrected.freq 0.450127
; min(P(S|M)) 6.57001e-30
; max(P(S|M)) 0.0100666
; proba_range 0.0100666
; Wmin -42.4
; Wmax 18.7
; Wrange 61.1
; logo file:/PurR.EcolK12_1nt_upstream.17.meme_quality_logo_m1.png
; logo file:/PurR.EcolK12_1nt_upstream.17.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161100
; Seconds 0.59
; user 0.59
; system 0.06
; cuser 0.44
; csystem 0.04