# Aligned ITS reference files

**URL:** <https://forum.mothur.org/t/aligned-its-reference-files/3124>\
**Category:** Commands in mothur\
**Created:** [February 12, 2017, 10:20am UTC](https://forum.mothur.org/t/aligned-its-reference-files/3124 "2017-02-12T10:20:04Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![jitendrakeshri](https://avatars.discourse-cdn.com/v4/letter/j/8e8cbc/32.png) [@jitendrakeshri](https://forum.mothur.org/u/jitendrakeshri)\
**Post date:** [February 12, 2017, 10:20am UTC](https://forum.mothur.org/t/aligned-its-reference-files/3124/1 "2017-02-12T10:20:04Z")

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Please suggest from where the ITS aligned reference fasta file can be downloaded?

I have tried from the link [https://www.mothur.org/wiki/UNITE\_ITS\_database](https://www.mothur.org/wiki/UNITE_ITS_database)

but the mothur returns at pcr.seq command with “seqs are not aligned. When using start and end your sequences must be aligned.”

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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:** [February 13, 2017, 1:04pm UTC](https://forum.mothur.org/t/aligned-its-reference-files/3124/2 "2017-02-13T13:04:39Z")

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Hi,

I’m not sure that a global pan-ITS reference alignment is possible since ITS fragments are rarely homologous even within a genome. You probably want to do something like pairwise.seqs ([https://mothur.org/wiki/Pairwise.seqs](https://mothur.org/wiki/Pairwise.seqs))

Pat