In JBrowse 2 there are multiple ways to obtain sequence information. One is via a context menu when region is selected by clicking and dragging on the “number line” part of the linear genome view:

Selecting “Get sequence” from the context menu will open a dialog where you will have a few options for how to get your sequence:

To get the sequence, you have the option to either save it as a file in your browser’s default download folder or you can copy the sequence to your clipboard.  Additionally, you can both complement and reverse the sequence before saving the sequence. Finally, note that the fasta header has the exact coordinates of the selected sequence so that you’ll know where the sequence came from.

The other way to get sequence information from JBrowse is by clicking on a feature. Clicking on a feature with start and end coordinates (that is, any features other than quantitative graphs) will open a “Feature details” panel that has one or more “Get sequence” buttons. For simple features (ie, features with no subfeatures), there will be one button and will present you with options to either show just the genomic region covered by the feature or show the genomic region plus 500 base pairs on either side of the feature.  You can also select whether you want to copy the “plain” fasta sequence, or the color highlighted sequence (“copy html”) which can then be pasted into a word processing tool that knows how to deal with html like Google Docs, which will preserve the color highlighting.

For more complex features that have subparts (things like similarity matches, but NOT genes–more on those later), there are several “Get sequence” buttons, one for the parent feature and then one each for the subfeatures.  For example, in the C. elegans “ESTs” track, you would see something like this:

Where the parent’s “Get sequence” button would get the genomic sequence that would cover the entire range of the feature and the subfeatures’ “Get sequence” button would just cover the range of that subfeature.

Finally, for gene or transcript features you once again have multiple options. In the details panel, there is a button for the gene as a whole that will get the genomic sequence as before. For each transcript, the sequence button has several more options to display thinks like the CDS or cDNA sequence, the genomic sequence with UTR and CDS regions highlighted, optionally with the introns truncated (so that you can see splice regions but the majority of the intron is replace with ellipses (“…”), or the in silico translation of the sequence.

Note that, as with many things in the JBrowse help docs, all of the methods of obtaining sequence here work both in the full JBrowse web application as well as in the embedded JBrowse that is on gene and other feature pages.