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