align.seqs deletes almost all bases

I’m working on a dataset which consists of sequences with 800 to 1000 bases. I use align.seqs and the silva database file you supply (silva.nr_v119.align).
mothur > align.seqs(candidate=XXX.fasta, template=silva.nr_v119.align, processors=2)

The sequences I get are very short (around 5 bases) or contain only dots.

… […]

Why does mothur delete my bases and how can I prevent this?

Is it possible your reads are backwards? You might try flip=T in align.seqs.


Thanks for the fast reply.

I’m gonna try this tomorrow and post here about the result.

The flip=T command doesen’t change anything.
The sequences still contain almost exclusively dots.

What type of sequences are you trying to align?