# align.seqs shortens some pyrosequences

**URL:** <https://forum.mothur.org/t/align-seqs-shortens-some-pyrosequences/1316>\
**Category:** Commands in mothur\
**Created:** [April 22, 2013, 1:10pm UTC](https://forum.mothur.org/t/align-seqs-shortens-some-pyrosequences/1316 "2013-04-22T13:10:13Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![igeorge](https://avatars.discourse-cdn.com/v4/letter/i/838e76/32.png) [@igeorge](https://forum.mothur.org/u/igeorge)\
**Post date:** [April 22, 2013, 1:10pm UTC](https://forum.mothur.org/t/align-seqs-shortens-some-pyrosequences/1316/1 "2013-04-22T13:10:13Z")

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Hi Pat,  
I am using Mothur to analyze microbial diversity in mangrove sediment samples. I noticed that the command “align.seqs” shortens considerably some sequences (a few thousands out of 106000).  
For example, in my all.trim.unique.fasta file, one sequence is AGTCCGGCTACCCATCAGAGCCTTGGTGAGCCGTTACCTCACCAACAAGCTAATAGGACATAGGCCGCTCCCCGGGCAGAGGGTTGCCCGACCGTTTACACTTCGGAAGATGCCATCCGAGGTGACCATCCGGTATTACCTGCCGTTTCCAGCAGCTATTCCGGTCCCGAGGGTACGTTGCCTATGTATTACTCACCCTTTCGCCGCTCTCCAGCACCCCGAAGGATGCCTTCGCGCTCGACTTGCATGCCTAAACCACGCCGCCAGCGTTCACT  
(275 bp in total)  
After alignment against the SILVA database (uploaded from the MOTHUR website):

> align.seqs(candidate=all.trim.unique.fasta, template=silva.bacteria.fasta, flip=t, processors=2)

the same sequence looks like this (in the all.trim.unique.align file) (12 bp in total)  
…CCAGCGTTCACT…

what is happening here? Should I use another reference database?  
thanks for your help,  
isabelle

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**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:** [April 23, 2013, 12:30pm UTC](https://forum.mothur.org/t/align-seqs-shortens-some-pyrosequences/1316/2 "2013-04-23T12:30:54Z")

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I suspect these are mostly garbage sequences. If you take that sequence and blast it against the GenBank nt database (exclude uncultureds) you’ll get a bunch of awful alignments. The top match is only 76% identical to some members of the Planctomycetales at the 5’ end of your sequence. While it’s entirely possible that you have a new domain of life, given your alignment, it is unlikely. Also, when I blasted the last 200 bp of your sequence there were no significant matches. I’d remove these bad aligners using screen.seqs and move on without worrying.

Pat