Fig 1.

Schematic overview of alpha satellite organization, assembly, and read depth analysis. The assembled alpha satellite is organized by sequence similarity. (a) Alpha satellite monomers from hg19 assembled chromosomes were evaluated for the presence of local homogenization in tandem, intrachromosomal homogenization patterns that are regional but not in tandem, and interchromosomal or interarray patterns (defined by pairwise identities of ≥95%). (b) In this study, homogenized monomers are then clustered, or “purposely collapsed,” as illustrated. As a result, a single region on the human assembly could represent a cluster of more than one monomer. (c) These multimonomer sites represent multicopy regions, as demonstrated by the elevated read depth estimates.