1. Set the method to use for prediction:
BLAST is used by default. MegaBLAST is presumably a bit faster.
2. Set Filter Options:
- Coverage(%): 95
- Identity(%): 95
- Word Size: 96
- E-Value: 1e-5
3. Set the number of segments to compare:
Each segment must be in a separate fast formatted file, or you can cut and paste one segment at a time. Each segment file can have any amount of sequences, as long as the sequences are all of the same segment. This also applies to cutting and pasting sequences into the text area. The Sample Data page shows examples of how to format the segments.