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  • Select the Tools ‣ Query Designer item in the main menu.

Result: The Query Designer window appears:



  • Drag the Repeats element from the Palette to the Scene.

Result: The Repeats element subunits are presented on the Scene:



Note, that by default minimum distance between left and right repeats is 0bp, the maximum distance is 5000bp.

  • Slide the Repeats element subunits apart.

Result:



  • Drag the ORF element from the Palette and drop it between the repeats.

Result: The ORF element is presented on the Scene:



  • Find the End-Start constraint on the Palette:


And drag it between the left Repeats element and ORF.

Result: The dialog appears:



  • Check that From equals to Repeats.left and To equals to ORF. Set Max to 5000. Press the OK button.

Result: The constraint has been added to the elements:



  • Repeat steps 5-6 for ORF element and the right Repeats subunit.

Result: The schema looks as follows:



  • Press the Run Schema button on the toolbar:


Result: The Run schema dialog appears:



  • Browse for the sequence to analyze (the Load sequence field) and for a GenBank file to save results to (the Save results to field). Click the Run button.

Result: Both the sequence and the file with annotations are added to the current project. The sequence appears in the Sequence View window, for example:



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To learn more about the Sequence View read main UGENE User Manual.

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The schema described in this example is also available as sample schema. Select the Samples tab on the Palette and double-click the ORF-Repeats to open the sample schema.

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