Examples of multiple hits in the RepeatMasker . out file corresponding to one copy. (A) Multiple hits due to separation between the LTR and internal regions in the consensus sequence in the Repeat Library for the LTR-retrotransposon Tirant in D. melanogaster. Three hits are obtained with RepeatMasker, which correspond to one complete copy. (B) Two large deletions lead to the identification of three hits in RepeatMasker corresponding to one incomplete copy of the Helena element in D. melanogaster. (C) Example of one TE inserted into another. The Quasimodo LTR-retrotransposon is inserted in the reverse orientation by a hobo element, which is incomplete due to an internal deletion. While six hits are proposed by RepeatMasker, they in fact correspond to two copies, one for each element. LTR, long terminal repeat; TE, transposable element.