OTU clusters

My fasta file has 1487 unique sequences and after doing a pairwise.seqs command followed by cluster command, the make.shared table showed that the first level of cutoff (unique label) had total numOTUs of 1480 instead of 1487. I don’t quite understand why? I am not sure if the numOtus at a unique cutoff are supposed to be the same as the total number of unique sequences in the fasta file?

Thank you,

The cluster command will place sequences in the same OTU at the unique level if the distance between them is 0.0. The pairwise.seqs command aligns the sequences to each other and then calculates the number of differences between the two fragments. The aligning parameters you set, the distance calculator you choose, whether you set countends can effect the alignment and distances mothur calculates.