## Description

This track shows syntenous (corresponding) regions between $o_organism and $organism chromosomes. The $o_date ($o_db) $o_organism assembly was used for this annotation.

## Methods

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 $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.

## Credits

Contact Robert Baertsch at UCSC for more information about this track. Thanks to the Mouse Genome Sequencing Consortium for providing the $organism sequence data.