# pcr.seqs command

**URL:** <https://forum.mothur.org/t/pcr-seqs-command/2117>\
**Category:** Commands in mothur\
**Created:** [November 5, 2014, 6:28pm UTC](https://forum.mothur.org/t/pcr-seqs-command/2117 "2014-11-05T18:28:54Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![pca](https://avatars.discourse-cdn.com/v4/letter/p/7ba0ec/32.png) [@pca](https://forum.mothur.org/u/pca)\
**Post date:** [November 5, 2014, 6:28pm UTC](https://forum.mothur.org/t/pcr-seqs-command/2117/1 "2014-11-05T18:28:54Z")

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Hi,

I had some samples that were taken from the human gut. I am now trying to run the mothur pipeline for the microbiome analysis of the data. For the command, pcr.seqs, how do I know the start and end positions for the alignment? Also, is the silva database the only database available?

thanks!

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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:** [November 11, 2014, 6:14pm UTC](https://forum.mothur.org/t/pcr-seqs-command/2117/2 "2014-11-11T18:14:42Z")

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> or the command, pcr.seqs, how do I know the start and end positions for the alignment?

This is a question we seem to answer a lot…  
[http://mothur.ltcmp.net/t/pcr-seqs-start-stop-for-v3-5-on-miseq/1608/2](http://mothur.ltcmp.net/t/pcr-seqs-start-stop-for-v3-5-on-miseq/1608/2)

> Also, is the silva database the only database available?

Although we only suggest using the SILVA reference alignment, other references are here:

> **[Alignment database](http://mothur.org/wiki/Alignment_database)**
>
> The website that supports the mothur software program - one of the most widely used tools for analyzing 16S rRNA gene sequence data. Step inside to learn how to use the software, get help, and join our community!

For classification the references are here:

> **[Taxonomy outline](http://mothur.org/wiki/Taxonomy_outline)**
>
> The website that supports the mothur software program - one of the most widely used tools for analyzing 16S rRNA gene sequence data. Step inside to learn how to use the software, get help, and join our community!