The telomere and subtelomere are repetitive sequences at the ends of chromosomes required for chromosome length preservation. In Drosophila, telomere and subtelomere are highly plastic; each of them varies in copy number and sequence both within and across species. In addition, there is evidence of functional crosstalk between telomere and subtelomere, suggesting that the two regions may co-evolve to maintain system fidelity. However, without characterizing the sequence of the subtelomere, we cannot investigate whether subtelomere evolution affects telomere function. This characterization has recently been made possible due to the advent of single-molecule sequencing, which can be used to assemble repetitive regions using long, 100 kilobase reads. Here, I begin to characterize the composition and variability of subtelomeric genes, focusing on exon duplications, intergenic distance variability, and functional open reading frame polymorphism. I find extensive polymorphisms in both exon copy number and presence-absence of functional open reading frames.