The chain track shows alignments of human ($date) to other genomes using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and the other genome simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.
The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the -human assembly or an insertion in the other assembly. +other assembly or an insertion in the human assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the other genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.
In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.
The net track shows the best human/other chain for