RegulonDB
XylR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/XylR/XylR.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 /XylR.EcolK12_1nt_upstream.21.meme_quality_logo
; Input files
; input /XylR.EcolK12_1nt_upstream.21.meme_quality_matrix.tf
; prior /XylR.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 /XylR.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 5 5 3 2 4 1 3 7 7 6 5 5 2 0 3 0 7 7 1 3 1
C 3 1 0 0 0 2 2 0 1 0 0 1 1 6 0 2 0 0 2 2 0
G 0 1 2 2 4 0 3 0 0 0 0 0 1 1 4 0 1 1 0 0 7
T 0 1 3 4 0 5 0 1 0 2 3 2 4 1 1 6 0 0 5 3 0
//
A 0.6 0.6 0.4 0.3 0.5 0.1 0.4 0.8 0.8 0.7 0.6 0.6 0.3 0.0 0.4 0.0 0.8 0.8 0.1 0.4 0.1
C 0.4 0.1 0.0 0.0 0.0 0.2 0.2 0.0 0.1 0.0 0.0 0.1 0.1 0.7 0.0 0.2 0.0 0.0 0.2 0.2 0.0
G 0.0 0.1 0.2 0.2 0.5 0.0 0.4 0.0 0.0 0.0 0.0 0.0 0.1 0.1 0.5 0.0 0.1 0.1 0.0 0.0 0.8
T 0.0 0.1 0.4 0.5 0.0 0.6 0.0 0.1 0.0 0.3 0.4 0.3 0.5 0.1 0.1 0.7 0.0 0.0 0.6 0.4 0.0
//
A 0.7 0.7 0.2 -0.1 0.5 -0.7 0.2 1.0 1.0 0.9 0.7 0.7 -0.1 -2.2 0.2 -2.2 1.0 1.0 -0.7 0.2 -0.7
C 0.5 -0.4 -2.2 -2.2 -2.2 0.2 0.2 -2.2 -0.4 -2.2 -2.2 -0.4 -0.4 1.2 -2.2 0.2 -2.2 -2.2 0.2 0.2 -2.2
G -2.2 -0.4 0.2 0.2 0.8 -2.2 0.6 -2.2 -2.2 -2.2 -2.2 -2.2 -0.4 -0.4 0.8 -2.2 -0.4 -0.4 -2.2 -2.2 1.4
T -2.2 -0.7 0.2 0.5 -2.2 0.7 -2.2 -0.7 -2.2 -0.2 0.2 -0.2 0.5 -0.7 -0.7 0.9 -2.2 -2.2 0.7 0.2 -2.2
//
A 0.4 0.4 0.1 -0.0 0.2 -0.1 0.1 0.8 0.8 0.6 0.4 0.4 -0.0 -0.1 0.1 -0.1 0.8 0.8 -0.1 0.1 -0.1
C 0.2 -0.1 -0.1 -0.1 -0.1 0.0 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.8 -0.1 0.0 -0.1 -0.1 0.0 0.0 -0.1
G -0.0 -0.1 0.0 0.0 0.4 -0.0 0.2 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1 -0.1 0.4 -0.0 -0.1 -0.1 -0.0 -0.0 1.1
T -0.1 -0.1 0.1 0.2 -0.1 0.4 -0.1 -0.1 -0.1 -0.0 0.1 -0.0 0.2 -0.1 -0.1 0.6 -0.1 -0.1 0.4 0.1 -0.1
//
; Sites 8
>site_0
CAGTGTGAAATAACATAATTG
>site_1
CATTGTAAAAAATGATAATTG
>site_2
ATAAACCAAAAATCGTAATCG
>site_3
AAAGATAAAAATCTGTAATTG
>site_4
ACTTGTGAATTATCTCAATAG
>site_5
CATGACAAAAACGCGTAACAA
>site_6
AAGTGTCTATAATCACGGCAG
>site_7
AGAAAAGACATTACGTAAACG
;
; Matrix parameters
; Number of sites 8
; 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 MADDRTVAAAWAWCRTAATHG
; AC MADDRTVAAAWAWCRTAATHG
; id MADDRTVAAAWAWCRTAATHG
; name MADDRTVAAAWAWCRTAATHG
; description madkryvAAawatCryAAyhG
; statistical_basis 8 sequences
; sites 8
; nb_sites 8
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 8.57938
; information.per.column 0.408542
; max.possible.info.per.col 1.58873
; consensus.strict aaatgtgAAaaatCgtAAtaG
; consensus.strict.rc CTATTACGATTTTTCACATTT
; consensus.IUPAC madkryvAAawatCryAAyhG
; consensus.IUPAC.rc CDRTTRYGATWTTTBRYMHTK
; consensus.regexp [ac]a[agt][gt][ag][ct][acg]AAa[at]atC[ag][ct]AA[ct][act]G
; consensus.regexp.rc C[AGT][AG]TT[AG][CT]GAT[AT]TTT[CGT][AG][CT][AC][ACT]T[GT]
; residues.content.crude.freq a:0.4583|c:0.1369|g:0.1607|t:0.2440
; G+C.content.crude.freq 0.297619
; residues.content.corrected.freq a:0.4397|c:0.1448|g:0.1655|t:0.2500
; G+C.content.corrected.freq 0.3103
; min(P(S|M)) 2.39642e-33
; max(P(S|M)) 1.1993e-05
; proba_range 1.1993e-05
; Wmin -43
; Wmax 16.2
; Wrange 59.2
; logo file:/XylR.EcolK12_1nt_upstream.21.meme_quality_logo_m1.png
; logo file:/XylR.EcolK12_1nt_upstream.21.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161129
; Job done 2019-06-03.161129
; Seconds 0.52
; user 0.52
; system 0.05
; cuser 0.4
; csystem 0.04