Since version 1.9.0 a new sequence analyze tool "Query Designer" is available in UGENE. This tool allows you to find sequence regions containing specified set of features.

For instance, you can search a sequence for open reading frames surrounded by repeat units using supplied sample query file as follows (post below contains pictures):

1. Open a sequence in the Sequence view.
2. Activate the context menu and select 'Analyze -> Analyze with query schema'. Pic.1
3. In the 'File with query' field select '$UGENE/data/query_samples/RepeatsWithORF.uql'. Pic.2
4. Click 'Search'.
5. Obtained annotations are collected in groups so that every group contains an ORF surrounded by repeat pair units. Pic.3

Any feedback is welcome.