The HIV virus has been sequenced 10's of thousands of times, and all those sequences are in the database that was searched. Likewise, there are thousands of cop

The HIV virus has been sequenced 10's of thousands of times, and all those sequences are in the database that was searched. Likewise, there are thousands of copies of the E. coli proteome in the sequence databases. The nr database, part of which was searched, is extremely redundant (despite the fact that 'nr' stands for "non-redundant" -- no two identical sequences). So unless you go to a lot of trouble (e.g. the NCBI landmark database), most sequence databases are a mixture of 10's to 10,000's of very closely related sequences (not a random sample), from a non-random sample of organisms (we tend to sequence pathogens). Protein and DNA sequence databases are very large, but they are not random.