Fig. 3
TE landscapes in D. melanogaster and D. simulans. For each TE fragment the divergence to consensus was estimated. For each TE order the total amount of DNA (in bp) is shown as a function of the percentage of divergence. The percentage of divergence to the consensus sequences is a proxy for age: old TEs have accumulated mutations, young TEs are similar to consensus sequences. RepeatMasker was used to recover TE fragments in genomic assemblies (same method as Figure 2 [100],). Percentages of divergence to consensus were evaluated from RepeatMasker output .align file using A. Kapusta script [154]