Active centromere locations were determined by identifying the CENH3 ChIP-seq-enriched regions in the final assembly using genomic reads as a control. The peak calling process was carried out by Epic2 (https://github.com/biocore-ntnu/epic2).
The coordinates of repeat arrays were identified by blasting consensus sequence against the genome and scaffolds.
The enrichment of mappable repeat elements in functional centromeres (CentC, CRMs, and five major TE families) were assessed.