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Why do I get the message "ERROR: Blast: ...

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Why do I get the message "ERROR: Blast: No valid letters to be indexed"?

You may have accidentally entered an accession number in the search box without changing the input selection from "Sequence in FASTA format" to "Accession or gi". You will also see this error message if too many ambiguity codes (R,Y,K,W,N, etc. fornucleotides) are present in your query sequence. Although BLAST allows ambiguity codes, be aware that these will always contribute a negative score in nucleic acid searches. Thus, sequences such as degenerate PCR primers with ambiguity codes maynot find any significant hits even though they may be designed from sequences that are present in the database.

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