This track shows syntenous (corresponding) regions between $organism and rat chromosomes.
We passed a 100k non-overlapping window over the genome and using the Blastz best in rat genome alignments - looked for high-scoring regions with at least 40% of the bases aligning with the same region in rat. 100k segments were joined together if they agreed in direction and were within 500 kb of each other in the $organism genome and within 4 Mb of each other in the rat. Gaps were joined between syntenic anchors if the bases between two flanking regions agreed with synteny (direction and rat location). Finally, we extended the syntenic block to include those areas.
Contact Robert Baertsch at UCSC for more information about this track.