Table 2.

Novel repeats or transposable elements found to be unique to each species.

Species	Novel element name	Novel element location(s)	Consensus length	Notes
D. virilis	rnd-1_family-95# LTR/Gypsy	Unplaced contigs tig00001890, tig00002154	11505 bp (mix of 1132 bp and 820 bp monomers)	Structured as a complex tandem repeat (the 820 bp monomer has an internal deletion compared to the 1132 bp monomer); homology to Gypsy is minimal.
D. virilis	rnd-1_family-144#LINE/I-Jockey	Unplaced contigs tig00001890, tig00001978, tig00002154, tig00002244, tig00003829, tig00003830	4834 bp	Highly similar to Repbase sequence HeT-A3_DVi, which covers 84% of the sequence at 99% identity. A gag domain is identifiable.
D. novamexicana	rnd-1_family-329#Unknown	Present on all Muller elements and a few unplaced contigs	346 bp	No conserved domains identifiable, no TSD identified from REPCLASS.
D. Americana	rnd-1_family-159#Unknown	Y contig tig00002773	767 bp	Likely the same element as below: overlaps 77 bp with below sequence and found in tandem with it.
D. Americana	rnd-1_family-109#DNA/hAT-Ac	Y contig tig00002773	421 bp