Level of conservation as measured by the FootPrinter program. Hits are clickable: they take you to the multiple alignment of the region clicked.
The score of each window of length 10 is evaluated as described here.
FootPrinter is a program by Mathieu Blanchette and Martin Tompa. Many thanks to Adam Siepel for the phylogenetic inferrences and to Webb Miller for providing the multiple alignment of the Zoo sequences.