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 missing sequence in the non-$organism species. Double lines represent gaps in the chain where sequence is present in both species but they do not align. In cases where there are multiple chains over a particular portion of the $organism genome, 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.
The display indicates the chromosome, strand, and location of the match for each matching alignment (in thousands).
Blastz was developed at Pennsylvania State University by Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison.
Lineage-specific repeats were identified by Arian Smit and his program RepeatMasker.
The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
The browser display and database storage of the chains were made by Robert Baertsch and Jim Kent.
Human-Mouse Alignments with BLASTZ. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler H, and Miller W. Genome Research 2003 Jan;13(1):103-7.
Scoring pairwise genomic sequence alignments. Chiaromonte F, Yap VB, Miller W. Pac Symp Biocomput 2002;:115-26.