## Description

This track shows duplicated regions of the genome. The percent identity of the duplicon is reflected in the level of gray in the graphic display. In the details page the 'score' is ten times the percent identity (excluding gaps).

## Methods

Blastz and axtChain were run on the $organism genome vs. itself to create gapped alignments. The chains were broken up at gaps of 10,000 bases or more. After this break up chains spanning less than 5,000 bases or where more than 50% of the bases were in gaps were discarded. This procedure avoids including old paralogous genes that are under selection in the set of duplicons.

## Credits

This track was created by Jim Kent.