Comparison between phyloMOD.pl and avid/Vista.
As you can notice peaks in Vista are identified by
module/hits in phyloMOD.pl.
In phyloMOD.pl output you can see both species coordinates while in Vista visualizations you have just one axis with coordinates for a single reference sequence (in this case mouse).
In the next picture you can see that modules can cross
each other since DNA bendability allows such a solution.
You can even notice that a potential regulatory region in the upstream region of mouse moved downstream in chicken.
Hence single hits are determined by local alignment
through bl2seq (blast two sequences) ans with subsequente computation
modules (or highly conserved regions) are detected.