RegulonDB
Nac matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/Nac/Nac.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 /Nac.EcolK12_1nt_upstream.17.meme_quality_logo
; Input files
; input /Nac.EcolK12_1nt_upstream.17.meme_quality_matrix.tf
; prior /Nac.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 /Nac.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 4 5 10 3 3 4 1 2 1 0 11 1 5 2 0 4 6
C 0 2 1 1 0 3 0 7 0 3 0 1 0 1 5 3 2
G 5 4 1 0 1 0 3 0 1 2 2 1 6 5 8 4 3
T 5 3 2 10 10 7 10 5 12 9 1 11 3 6 1 3 3
//
A 0.3 0.4 0.7 0.2 0.2 0.3 0.1 0.2 0.1 0.0 0.8 0.1 0.4 0.2 0.0 0.3 0.4
C 0.0 0.1 0.1 0.1 0.0 0.2 0.0 0.5 0.0 0.2 0.0 0.1 0.0 0.1 0.3 0.2 0.1
G 0.3 0.3 0.1 0.0 0.1 0.0 0.2 0.0 0.1 0.1 0.1 0.1 0.4 0.3 0.5 0.3 0.2
T 0.4 0.2 0.2 0.7 0.7 0.5 0.7 0.4 0.8 0.6 0.1 0.8 0.2 0.4 0.1 0.2 0.2
//
A -0.0 0.2 0.9 -0.3 -0.3 -0.0 -1.2 -0.6 -1.2 -2.7 1.0 -1.2 0.2 -0.6 -2.7 -0.0 0.4
C -2.7 -0.3 -0.9 -0.9 -2.7 0.0 -2.7 0.8 -2.7 0.0 -2.7 -0.9 -2.7 -0.9 0.5 0.0 -0.3
G 0.5 0.3 -0.9 -2.7 -0.9 -2.7 0.0 -2.7 -0.9 -0.3 -0.3 -0.9 0.7 0.5 1.0 0.3 0.0
T 0.2 -0.3 -0.7 0.8 0.8 0.5 0.8 0.2 1.0 0.7 -1.2 0.9 -0.3 0.3 -1.2 -0.3 -0.3
//
A -0.0 0.1 0.6 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 0.7 -0.1 0.1 -0.1 -0.1 -0.0 0.2
C -0.0 -0.1 -0.1 -0.1 -0.0 0.0 -0.0 0.4 -0.0 0.0 -0.0 -0.1 -0.0 -0.1 0.2 0.0 -0.1
G 0.2 0.1 -0.1 -0.0 -0.1 -0.0 0.0 -0.0 -0.1 -0.0 -0.0 -0.1 0.3 0.2 0.5 0.1 0.0
T 0.1 -0.1 -0.1 0.6 0.6 0.2 0.6 0.1 0.8 0.5 -0.1 0.7 -0.1 0.1 -0.1 -0.1 -0.1
//
; Sites 14
>site_0
GGATTTTCTTATGCGGA
>site_1
AAATTTTCTCAGGGGCG
>site_2
GGAATTGCTGATGTCGC
>site_3
TTATTTTTTGATATGTT
>site_4
ATAATCTCTTATTTGAC
>site_5
TATATTTTTTATATGAA
>site_6
TGATTATTGCATGTGTG
>site_7
AGCTTCGTTTATTGCAA
>site_8
GAGTAATCTCATAACCA
>site_9
TCATTCTATTTTAGCCT
>site_10
GATTGTGCTTATGTTGT
>site_11
AAATAATATTGCGGCAA
>site_12
GTATTAATATATAAGGG
>site_13
TCACATTCTTGATGGTA
;
; Matrix parameters
; Number of sites 14
; 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 DDATTWTYTTATDKSND
; AC DDATTWTYTTATDKSND
; id DDATTWTYTTATDKSND
; name DDATTWTYTTATDKSND
; description krattykyTyatrkssr
; statistical_basis 14 sequences
; sites 14
; nb_sites 14
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 5.33261
; information.per.column 0.313683
; max.possible.info.per.col 1.58873
; consensus.strict ggattttcTtatgggga
; consensus.strict.rc TCCCCATAAGAAAATCC
; consensus.IUPAC krattykyTyatrkssr
; consensus.IUPAC.rc YSSMYATRARMRAATYM
; consensus.regexp [gt][ag]att[ct][gt][ct]T[ct]at[ag][gt][cg][cg][ag]
; consensus.regexp.rc [CT][CG][CG][AC][CT]AT[AG]A[AG][AC][AG]AAT[CT][AC]
; residues.content.crude.freq a:0.2605|c:0.1218|g:0.1933|t:0.4244
; G+C.content.crude.freq 0.315126
; residues.content.corrected.freq a:0.2625|c:0.1276|g:0.1940|t:0.4159
; G+C.content.corrected.freq 0.321567
; min(P(S|M)) 1.60052e-26
; max(P(S|M)) 2.12145e-05
; proba_range 2.12145e-05
; Wmin -33.9
; Wmax 12.1
; Wrange 46
; logo file:/Nac.EcolK12_1nt_upstream.17.meme_quality_logo_m1.png
; logo file:/Nac.EcolK12_1nt_upstream.17.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161030
; Job done 2019-06-03.161030
; Seconds 0.52
; user 0.52
; system 0.06
; cuser 0.4
; csystem 0.05