It is a fairly old feature, but it still works. The functionality is documented here.

There is also an example file "tests/data/base_pairing/XdecoderStructure.gff" on github that you can test out, see https://github.com/GMOD/jbrowse/tree/master/tests/data/base_pairing

Loading script

bin/prepare-refseqs.pl --fasta tests/data/base_pairing/mahoney.fa
bin/draw-basepair-track.pl --gff tests/data/base_pairing/XdecoderStructure.gff

(must have GD::Image perl installed)

Example base pairing track

The original motivating application was to show patterns of base pairing in RNA secondary structures.