Our approach relies upon standalone BLAST and is very similar in concept to MaskerAid (Bedell et al., 2000). The default repeat masking parameters below, which are used during MAGI assemblies, have been optimized for use in maize (Emrich et al, 2004). No gain in masking efficiency was achieved using a more traditional sequence alignment algorithm (e.g., Smith-Waterman) instead of BLAST. The current repeat database for this feature includes sequences from four distinct sources. Full details about this database are available here and we ask that credit is given to each of these contributors whenever possible. Because our SDRs mostly consist of predicted repetitive sequences, we have provided an option to use this database alone for comparison.