Multiple blast hits in single genome - what could be the cause

[barnacules]

Hello,

I am searching a database of genomes for specific genes using BLAST.

In one genome of interest there are several BLAST hits with strong e-values - one with 100% homology to the query sequence.

I'm just trying to figure out what the cause could be; recombination or LGT? Processing error?

Thanks,
Pete

[GenoMax]

There may be multiple copies of the gene(s) in the genome at different locations. Some of the "hits" could be to similar domains, if they are not full length.

[barnacules]

Is this something I can verify?

There's only one copy of it annotated via Prokka, but I'm not sure if this would necessarily annotate multiple copies of the same gene.

[GenoMax]

Are those multiple blast hits discrete (when you look at the co-ordinates) or are they overlapping (you may be looking at multiple HSP in that case). If you expect only one copy of the gene then the hit with 100% homology may be the full length gene and others may be for domains that are shared by other genes.