Nonallelic homologous recombination (NAHR) between duplicated segments initiates the BFB cycles (model). Duplicated segments within a complex region could adopt a complex secondary structure that can impose an obstacle for the progression of replication forks and would generate a DSB. The 5'- to 3'-end resection of a DSB exposes single-stranded DNA that would fold back and anneal between inverted repeat sequences (intrastrand annealing). BIR (break-induced replication) would prime DNA synthesis and fill the single-stranded gap to create a chromosome with a hairpin-capped end. The replication of the chromosome would generate a dicentric chromosome that initiates the BFB cycles.