During macronuclear development in the ciliate Tetrahymena thermophila, extensive rearrangement events occur as DNA deletions. We have studied a developmentally programmed deletion called mse2.9 that occurs within an intron in a gene in both genomic DNA and in an rDNA vector introduced into the cell by transformation. Extensive microheterogeneity at the deletion junctions has been found in caryonidal strains and in the rDNA in transformed cells. A transformation assay has been used to identify sequences required for proper processing of mse2.9. Models to explain deletion site selection as well as microheterogeneity at junction sites are presented.