# aligning sequences to SILVA bacterial reference database
**URL:** https://forum.mothur.org/t/aligning-sequences-to-silva-bacterial-reference-database/3533
**Category:** Commands in mothur
**Created:** [August 1, 2018, 3:34pm UTC](https://forum.mothur.org/t/aligning-sequences-to-silva-bacterial-reference-database/3533 "2018-08-01T15:34:39Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@udesilva](https://forum.mothur.org/u/udesilva)
#### Post date: [August 1, 2018, 3:34pm UTC](https://forum.mothur.org/t/aligning-sequences-to-silva-bacterial-reference-database/3533/1 "2018-08-01T15:34:39Z")
Hi,
I get the below warning when I try to align my contigs to the SILVA bacterial reference database (silva.bacteria.fasta/silva.v4.fasta).
“[WARNING]: 249594 of your sequences generated alignments that eliminated too many bases, a list is provided in F:\Normal\_Mare\_Project\Data\_2\stability.trim.contigs.good.unique.flip.accnos.
[NOTE]: 121800 of your sequences were reversed to produce a better alignment.”
Would greatly appreciate if someone can help me with this.
Thank you.
---
### Author:  [@Kendra](https://forum.mothur.org/u/Kendra)
#### Post date: [August 3, 2018, 8:41pm UTC](https://forum.mothur.org/t/aligning-sequences-to-silva-bacterial-reference-database/3533/2 "2018-08-03T20:41:57Z")
it’s a warning, not an error so you may not need to do anything.
the ones that eliminated too many bases are likely bad though that’s a pretty big number so I’d be a little suspicious. flipping the seqs is usually fine unless you know that your seqs are all 5’-\>3’