Additional data file 2.

Duplicon modules were defined by processing the results of BLAST searches of in-house curated subtelomere query sequences (see text and Materials and methods). Colinear and properly oriented pairs of BLAST matches to the query sequence were joined into a chain if not separated by greater than 25 kb and not uninterrupted by other hits from the same query sequence. Groups of chained blast hits spanning ≥1 kb of the subject sequence were defined as duplicons. These methods were tolerant of insertions and deletions <25 kb in size (for example, of retrotransposons) but not tolerant of rearrangements.

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Ambrosini et al. Genome Biology 2007 8:R151   doi:10.1186/gb-2007-8-7-r151