Repeat analysis of D. virilis contigs compared to the D. melanogaster genome. The repeat density, defined as the percentage of total sequence (in base-pairs) that has been annotated as repetitive has been calculated using the D. virilis fosmid sequence obtained in this study and homologous regions from D. melanogaster (see Materials and methods). D. melanogaster and D. virilis have a very similar low repeat density on the major chromosome arms, and a similar but much higher repeat density on the dot chromosomes. (a) Percent repeat for each type identified by RepeatMasker using RebBase 8.12 with additional repeats identified in a BLASTN all-by-all comparison of the fosmid sequences presented here. (b) Percent repeat for each type identified by RepeatMasker using the Superlibrary (see text for description). The dot chromosome of D. melanogaster has about three times more DNA transposon sequence than does the D. virilis dot chromosome. 'Unknown' repeats are those from both RebBase 8.12 and the D. virilis PILER-DF library that have not been classified as to type.
Slawson et al. Genome Biology 2006 7:R15 doi:10.1186/gb-2006-7-2-r15