How are bases dropped during align.seqs

I’m just looking for a little clarification on how & why bases are dropped from candidate sequence reads during align.seqs


Only if they align to a base beyond the reference. If you’re using the silva.bacteria.fasta reference that would only happen if they align to the region before 1044 or after 43217 (or whatever it is). If there isn’t a good alignment (like not being from a 16S), then the whole sequence will likely get trimmed.