Each result annotation found with the remote BLAST in UGENE has a qualifier that specifies ID of the sequence. The prompt way to fetch sequences of several annotations is the following: select the annotations in the Annotations Editor, open the context menu, and choose the Fetch sequences from remote database->Fetch sequences by 'id' from 'blast result' item or Fetch sequences from remote database->Fetch sequences by 'accession' from 'blast result' item. The following dialog will appear:
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