Intramolecular transposition produces replicon dissociation in a bireplicon; this reaction is homologous to the well-characterized IS-associated deletions in the case of a monoreplicon. However the frequencies at which these two reactions occur differ by a factor of more than 10(2) in favor of deletion formation. This raises the question of how these deletions occur. We show that the presence of a productive replication on the fragment to be deleted interferes with deletion formation. Our results also suggest that the deleted fragment is not degraded during deletion formation.