The first step in the formation of the macronucleus is the removal of internal eliminated sequences (IES) and transposable elements (Tec). The chromosomes are then fragmented and telomeres added to the ends of the fragments that are going to be retained. These fragments are then replicated (ie, amplified).
Jacobs, M.E., and Klobutcher, L.A. 1996. The long and the short of developmental DNA deletion in Euplotes crassus.
J. Euk. Microbiol. 43, 442-452.