I'm having trouble to understand the meaning of having overlapping HSP after a BLAST.
The thing is: i have a sequence from NGS (Illumina Miseq) and assembled with SPAdes 3.6. When i BLAST it i got overlapping HPS. The contig i get is a bit bigger (around a hundred nucleotides) than the BLAST hit indeed, but since HPSs overlapp, shouldn't they have been assembled previously? i mean is that an assembly issue(/error) or something else?