From the degenerate nucleotide codes only N is accepted. Please note that protein queries, with too many nucleotide-like code (A,C,G,T,N) may also cause problems.
If you were running a protein blast query and then you want to run a nucleotide query, is better to reset the form (click reset button), to avoid misscalculations
The BLAST search will not accept "-" in the query. To represent gaps, use a string of N (nucleotides) or X (proteins) instead.
Each sequence must have an identifier, ID lines must start with an ">".
Default expected value (evalue) is 1e-5, consider to increase this value to get more precise results.
If you upload a fasta file and also have pasted sequences in the text area, when you run blast it will only take in count the file uploaded.