Does Araport have a function identical to SEQVIEW, which provides the exact location of a sequence in an annotated view of the genome, complete with T-DNA insertions sites, cDNAs etc? This is a very useful tool. At the moment, it appears that you can only BLAST derived databases (e.g. coding sequences, UTRs etc), not the assembled, annotated genome sequence. JBrowse does not allow searches with a sequence, as SEQVIEW does.
JBrowse offers "Add sequence search track" that allows users to search for short sequences
This function, Add sequence search track, is under the "Track" in the top menu bar. With the gene model and T-DNA tracks on, users can search for short sequences such as primers and/or motifs and create a new track to display the locations and orientation of the query sequence in the annotated view. This 90-second video will walk you through this feature in JBrowse.