# problem of OTUs

**URL:** <https://forum.mothur.org/t/problem-of-otus/234>\
**Category:** mothur bugs\
**Created:** [May 24, 2010, 12:58pm UTC](https://forum.mothur.org/t/problem-of-otus/234 "2010-05-24T12:58:52Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![lee\_samuel](https://avatars.discourse-cdn.com/v4/letter/l/e9c0ed/32.png) [@lee\_samuel](https://forum.mothur.org/u/lee_samuel)\
**Post date:** [May 24, 2010, 12:58pm UTC](https://forum.mothur.org/t/problem-of-otus/234/1 "2010-05-24T12:58:52Z")

</div>

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~

---

<div class="post-metadata">

**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [May 24, 2010, 4:30pm UTC](https://forum.mothur.org/t/problem-of-otus/234/2 "2010-05-24T16:30:35Z")

</div>

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.