Figure 1.

Dynamic programming (SAPF) and MCMC (BigFoot) predictions along with annotated binding sites for the eve stripe 2 enhancer. For each nucleotide in the D. melanogaster sequence, both programs output the probability that the nucleotide was generated by a functional (slow) state. Experimentally verified binding sites in D. melanogaster for the transcription factors, Bicoid (BC), Hunchback (HB), Kruppel (KR), Giant (GT), and Sloppy-paired 1 (Sl1) are shown above the posterior probabilities.