This track shows syntenous (corresponding) regions between $organism and $o_organism chromosomes. The $o_date ($o_db) assembly of the $o_organism genome was used to produce this annotation.
We passed a 100k non-overlapping window over the genome and - using the blastz best-in-$o_organism genome alignments - looked for high-scoring regions with at least 40% of the bases aligning with the same region in $o_organism. 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 $o_organism. Gaps were joined between syntenic anchors if the bases between two flanking regions agreed with synteny (direction and $o_organism location). Finally, we extended the syntenic block to include those areas.
Contact Robert Baertsch at UCSC for more information about this track.