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.

Documentation on creating and editing query file using GUI interface or text editor is available at:
http://ugene.unipro.ru/documentation/qd_manual/index.html

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Petr Golubev wrote on Jan 19^th, 2011 at 7:05pm:

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.

Both explanations are very clear and helpful. I have successfully did all the steps by the help of this threat thanks a lot! :)