For a single sequence:
* Save all sequences you'd like to search for into a FASTA file like this:
    Quote:

* Open the sequence (e.g. a plasmid) in the UGENE Sequence View.
* Open the "Search in Sequence" tab on the Options Panel. The quickest way to do it is to use Ctrl+F hotkey (or Cmd+F on macOS).
* Check "Load patterns from file" and browse for the FASTA file.

You should now see the number of found results below. And you can save the results by clicking the "Create annotations" button. If you additionally check "Use pattern name" option in the "Annotation parameters" group, the sequences names in the FASTA file will be used to name the result annotations.

If you'd like to analyze several plasmid sequences at once, you may run a workflow that will do the job, see e.g. "Find pattern" sample workflow. Feel free to ask additional questions, if any.