Characteristics of core elements. (A) Comparison of known repeats in CNV-type and constant-type core elements. Average proportions of the known repeats, classified into six categories (SINE, LINE, LTR, DNA transposon (DNA), simple/satellite repeats (Simple/Sat), and unknown repeats) in each core element were compared between the CNV and constant types of core element. *, P < 0.05; **, P < 0.001. Average proportions were calculated from the proportion of each type of repeat in each type of core element. (B) Comparison of divergence between CNV-type and constant-type core elements. Divergence is represented by percentage values for the number of mutations and insertions or deletions that were detected after pairwise comparison of’ sequences. (C) Correlation between the divergence of the sequences and the number of duplications of core elements. Core elements 177 and 254 were excluded from these analyses because their sequences are contained within core elements 541 and 244, respectively.