EMMA (Evolutionary Model-based cis-regulatory Module Analysis) is meant for prediction of regulatory targets of a motif using two-species comparison. If you have a sequence window of length ~100 bp – 2000 bp, and its orthologous window from another species, use EMMA to score the window for matches to a given motif. EMMA is also useful for alignment of cis-regulatory modules (enhancers) between two species, if you have knowledge of the relevant transcription factor motifs.
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LoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299.
Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.
He X, Ling X, Sinha S.