# Sequence track

**TL;DR:** The sequence track appears automatically when an assembly is loaded,
showing the reference sequence and a six-frame translation (three frames per
strand), visible only at base resolution. If the view is horizontally flipped,
the sequence is shown reverse-complemented and the forward/reverse strand rows
swap places.

By default the translation uses the standard genetic code (NCBI table 1). If the
assembly config maps a reference sequence to a different genetic code (for
example a mitochondrial contig), the translation rows for that sequence use the
matching codon table. See
[Configuring alternative genetic codes](https://jbrowse.org/jb2-staging/docs/config_guides/assemblies/#configuring-alternative-genetic-codes-translation-tables)
for how to set this up.

You can also extract or copy the sequence underlying selected features; see the
[](https://jbrowse.org/jb2-staging/docs/user_guides/feature_sequence) guide.

<Figure caption="The sequence track showing the reference sequence (top row) and six-frame translation (three frames per strand) at single-base resolution." src="/img/sequence_track.png" />

Searching the reference sequence for a pattern, CRISPR guide, or restriction
site is a view-level feature; see [](https://jbrowse.org/jb2-staging/docs/user_guides/sequence_search).

## Getting the sequence out

The track menu's **Launch → Get sequence (visible region)** opens the sequence
for the window as FASTA, with reverse and complement toggles and a download. A
[rubberband selection](https://jbrowse.org/jb2-staging/docs/user_guides/basic_usage#rubberband-selection) opens
the same panel for a span narrower than the window.

## See also

- [](https://jbrowse.org/jb2-staging/docs/user_guides/gene_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/feature_sequence)
- [Assembly configuration](https://jbrowse.org/jb2-staging/docs/config_guides/assemblies)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/gc_content_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/sequence_search)