Get the names/accession numbers of the plasmids from PlasmidSeeker results.

Then BLASTn them against your sample, making your sample the subject and the reference is the query.

The alignment will show you exactly where is it in the areas that are identical to the reference.

Then, identify annotated genes from your plasmid that haven't showed up in the alignment, which could be not available in the reference, but present in your sample.