31) Multiple sequence titles in the same BLAST hit

We were curious about what it means when BLAST returns a BLAST hit indicated by a “>” but followed by multiple entries with different accession numbers.

Are these sequences the same? And are they the same only at the aligned region or in the rest of the sequence as well?

I did a check on how these sequences are related. Based on several examples (two listed below), for now, it could be concluded that these entries that fall under the same BLAST hit are full sequence duplicates. However, in terms of annotations they could be from different isolates.

Case 1: 2 accession numbers under the same BLAST hit

Alignment between full sequences of Q6R325.1 and AAS01728.1

• 100% identity, i.e. full sequences are exactly the same
• Same author
• Swissprot entry (Q6R325.1) has cross-reference to Genbank entry (AAS01728.1)

Case 2: Multiple accession numbers under the same BLAST hit

Multiple alignment of full sequences of all sequence titles

• Perfect alignment
• Same author
• Only the isolate annotation is different