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Table 2 Frequency of motifs in combined promoter sequences (CPS) in Xenopus tropicalis 4.2 genome ( apelen ≥ 10, motifgap ≤ 20)

From: APTE: identification of indirect read-out A-DNA promoter elements in genomes

Motif

CCAAT

GGGCGG

AGATA

TGATA

Genes with motif within 500 bp upstream of TSSa

13,255

2,531

12,703

12,201

Total number of motifs in genome

1,814,253

108,168

1,918,291

1,617,806

Motifs within 500 bp upstream of TSS (including multiples)

25,253 (1.39%)

3,377 (3.12%)

23,471 (1.22%)

20,927 (1.29%)

Motifs in CPS

3,771 (0.21%)

1,080 (1.00%)

2,351 (0.12%)

2,707 (0.17%)

Motifs in CPS within 500 bp upstream of TSS

36 (0.002%)

13 (0.012%)

18 (0.001%)

19 (0.001%)

  1. aTranscription Start Site.