problem of OTUs

I use the command “dist.seqs”, “read.otu” and “cluster” to get OTUs. And the bin.seqs command to get the OTUs sequences. However I found that the sequences in an OTU are not consistent with the parameters I want.

For example I set the cutoff=0.03, however, I found there are sequences with different length in one OTU; One of the sequences in the OTU is 60bp, while the others are 53bp. Is that the bug of MOTHUR, or I just misunderstood the construction of distance matrix? Thank you~

by default mothur will ignore overhangs at the 5 and 3’ ends. So if your sequences are identical for 53 bases, this is possible. I encourage people to use filter.seqs with trump=. to make sure sequences are flushed at the ends.