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De novo motif analysis for top putative enhancer-like regions. a Motif analysis of top 1600 putative enhancer-like regions using HOMER [32]. Using 100 bp windows, identified the CAGGTAG motif (Zelda binding site, p < 1e−40), a second motif (p < 1e−18, possibly related to Caudal or Abd-B), and poly(GA), bound by GAGA factor (p < 1e−17; GAF, Trl). b Similar motif analysis for 2000 early Zelda peaks and (C) ~6000 GAF sites
