The Query Designer allows a molecular biologist to analyze a nucleotide sequence using different algorithms (Repeats finder, ORF finder, Weight matrix matching, etc.) at the same time imposing constraints on the positional relationship of the results obtained from the algorithms.
A user-friendly interface is used to create a schema of the algorithms and constraints.
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Alternatively, you can create / edit a schema using a text editor.
When the schema has been created and all its parameters have been set you can run it for a nucleotide sequence. The results are saved as a set of annotations to the specified file in the Genbank format.
To learn more about the Query Designer read the Query Designer Manual (follow the link on the UGENE documentation page)