unique.seqs for identical but varying length reads

Commands in mothur
1

Here, even though Read1 and Read2 are 100%identical to Read3 (but length is 1 and 2 bases shorter respectively), unique.seqs will identify them as 3 unique sequences.

Read1: AAGGGCAATGCCGCTTGTAAAGCTCTTTCGT
Read2: AAGGGCAATGCCGCTTGTAAAGCTCTTTCGTC
Read3: AAGGGCAATGCCGCTTGTAAAGCTCTTTCGTCG

Is there a way to treat (or get an output) them as a single unique in mothur?
I thought of pre.cluster, but with longer reads, it will not produce desired output

Thanks for your help
Raman

2

Nope. Those are three unique sequences. You could align them, run filter.seqs(trump=.), and unique.seqs and they would be one sequence.

3

Thanks a lot, Pat.