Retrotransposons are a class of mobile genetic elements that make up around 40% of the sequenced mammalian genome (Chinwalla et al. 2002; Lander et al. 2001). Retrotransposons contribute to genomic instability in mammalian genomes by providing interspersed repeats of homologous sequences that can act as substrates for recombination causing deletions, duplications and structural rearrangements in the genome (Romanish et al. 2010). Retrotransposons are thought to be the only active class of mobile genetic element in most mammalian genomes, and can also cause genome instability through jumping to new locations in the genome. These de novo retrotransposon insertions have been reported as the causal mutation in various human genetic diseases (Crichton et al. 2014; Hancks and Kazazian 2012). The copy-and-paste mechanism that retrotransposons use to jump to new locations in the genome involves reverse-transcription of retrotransposon RNA, and integration of the resulting cDNA into new locations in the genome. There are typically a few hundred different types of retrotransposon annotated in each mammalian genome, with each type of retrotransposon being present in up to 10,000 copies. However, the types of retrotransposon, their copy numbers and their genomic locations vary signifcantly between species.