The help document answers the following questions:
Repeat masking filters are especially useful when searching with genomic sequence. You can choose from among the following programs:
Program What it masks RepeatMasker Low-complexity and interspersed repeats in nucleotide sequences using species-specific repeat libraries 1 DUST Simple repeats in nucleotide when searching nucleotide sequence databases with BLASTN2 SEG Low-complexity regions in protein sequences 3 XNU Short tandem repeats in protein sequences 4.
RepeatMasker filters out repetitive sequences using a set of scoring matrices specific to rodent, primate, other mammals, Drosophila, or Arabidopsis thaliana repeats. You can run RepeatMasker with one of these scoring matrices to mask repetitive sequences in your query sequence before running WU-BLAST. If RepeatMasker finds repetitive regions in the sequence, it replaces those nucleotide symbols with N.
See RepeatMasker Output for a table describing the location and identity of repeats that RepeatMasker finds.
For more information and documentation on RepeatMasker, see http://www.repeatmasker.org/.