This is a graph of the amount of pile-up alignments we are getting when monDom4 is aligned to Hg18 on just chr22. The graph height at any particular location is a count of the number of different monDom4 alignments overlapping at that chr22 position in Hg18. There are three hot spots on Hg18 chr22 with thousands of hits from monDom4. Namely:
It hasn't been measured, but I would expect similar patterns on other Hg18 chromosomes since our alignment counts on Hg18 are immense. This is just a sample from chr22 since it is small and easy to measure.
The data and presentation of this graph were prepared by Hiram Clawson.