Double-stranded Illumina DNA libraries were built according to the methods previously described (13, 14, 31), with some minor modifications in the Taq polymerase used for amplification. Libraries built from different samples were amplified using different polymerases (table S2). All libraries were screened on a Bioanalyzer 2100 (Agilent) to ensure that the DNA length distributions did not show any significant artifacts from amplification, e.g., artificially long molecules due to serial binding or primer dimers. Where these problems occurred, the number of PCR amplification cycles or primer concentration was adjusted. All PCR and extraction blanks were screened for contaminant library constructs on the Bioanalyzer.

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