RegulonDB
AsnC matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/AsnC/AsnC.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 /AsnC.EcolK12_1nt_upstream.17.meme_quality_logo
; Input files
; input /AsnC.EcolK12_1nt_upstream.17.meme_quality_matrix.tf
; prior /AsnC.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 /AsnC.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 0 0 4 1 0 1 3 1 0 4 3 3 4 3 3 2 3
C 0 2 0 0 0 3 1 0 2 0 0 1 0 0 0 1 1
G 0 2 0 0 0 0 0 2 0 0 0 0 0 1 1 1 0
T 4 0 0 3 4 0 0 1 2 0 1 0 0 0 0 0 0
//
A 0.1 0.1 0.9 0.3 0.1 0.3 0.7 0.3 0.1 0.9 0.7 0.7 0.9 0.7 0.7 0.5 0.7
C 0.0 0.4 0.0 0.0 0.0 0.6 0.2 0.0 0.4 0.0 0.0 0.2 0.0 0.0 0.0 0.2 0.2
G 0.0 0.4 0.0 0.0 0.0 0.0 0.0 0.4 0.0 0.0 0.0 0.0 0.0 0.2 0.2 0.2 0.0
T 0.9 0.1 0.1 0.7 0.9 0.1 0.1 0.3 0.5 0.1 0.3 0.1 0.1 0.1 0.1 0.1 0.1
//
A -1.6 -1.6 1.1 -0.1 -1.6 -0.1 0.8 -0.1 -1.6 1.1 0.8 0.8 1.1 0.8 0.8 0.5 0.8
C -1.6 0.8 -1.6 -1.6 -1.6 1.1 0.2 -1.6 0.8 -1.6 -1.6 0.2 -1.6 -1.6 -1.6 0.2 0.2
G -1.6 0.8 -1.6 -1.6 -1.6 -1.6 -1.6 0.8 -1.6 -1.6 -1.6 -1.6 -1.6 0.2 0.2 0.2 -1.6
T 1.1 -1.6 -1.6 0.8 1.1 -1.6 -1.6 -0.1 0.4 -1.6 -0.1 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6
//
A -0.1 -0.1 0.9 -0.0 -0.1 -0.0 0.5 -0.0 -0.1 0.9 0.5 0.5 0.9 0.5 0.5 0.2 0.5
C -0.1 0.3 -0.1 -0.1 -0.1 0.7 0.0 -0.1 0.3 -0.1 -0.1 0.0 -0.1 -0.1 -0.1 0.0 0.0
G -0.1 0.3 -0.1 -0.1 -0.1 -0.1 -0.1 0.3 -0.1 -0.1 -0.1 -0.1 -0.1 0.0 0.0 0.0 -0.1
T 0.9 -0.1 -0.1 0.5 0.9 -0.1 -0.1 -0.0 0.2 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
//
; Sites 4
>site_0
TGATTCATTAAAAAAGA
>site_1
TGATTAAGCAACAAAAA
>site_2
TCATTCAATAAAAAGCC
>site_3
TCAATCCGCATAAGAAA
;
; Matrix parameters
; Number of sites 4
; 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 TSATTCADYAAAAAAVA
; AC TSATTCADYAAAAAAVA
; id TSATTCADYAAAAAAVA
; name TSATTCADYAAAAAAVA
; description TsAtTCmgyAamArrvm
; statistical_basis 4 sequences
; sites 4
; nb_sites 4
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 8.05439
; information.per.column 0.473788
; max.possible.info.per.col 1.58873
; consensus.strict TgAtTCagcAaaAaaaa
; consensus.strict.rc TTTTTTTTGCTGAATCA
; consensus.IUPAC TsAtTCmgyAamArrvm
; consensus.IUPAC.rc KBYYTKTTRCKGAATSA
; consensus.regexp T[cg]AtTC[ac]g[ct]Aa[ac]A[ag][ag][acg][ac]
; consensus.regexp.rc [GT][CGT][CT][CT]T[GT]TT[AG]C[GT]GAAT[CG]A
; residues.content.crude.freq a:0.5147|c:0.1618|g:0.1029|t:0.2206
; G+C.content.crude.freq 0.264706
; residues.content.corrected.freq a:0.4700|c:0.1709|g:0.1232|t:0.2359
; G+C.content.corrected.freq 0.294114
; min(P(S|M)) 5.3241e-24
; max(P(S|M)) 0.000657966
; proba_range 0.000657966
; Wmin -27.4
; Wmax 15
; Wrange 42.4
; logo file:/AsnC.EcolK12_1nt_upstream.17.meme_quality_logo_m1.png
; logo file:/AsnC.EcolK12_1nt_upstream.17.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.61
; user 0.61
; system 0.06
; cuser 0.42
; csystem 0.05