Blast

https://blast.ncbi.nlm.nih.gov/Blast.cgi

• E value: the number of hits expected by chance (from this query to this database)
• is not a probability, so can be greater than 1
• 1E-6 is good
• 0.0 means no chance of hitting this result by chance with this query and this database
• takes into account the length of the query but not the size of the database, so the database affects it
• Blast uses a seed: e.g. 12 bases - does an exact match to everything in the database - then finds colocated seeds, then does proper alignment