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- Left window - annotations to search intersection regions for.
- Right window - the list of possible intersection regions.
- Region size - the length of the new intersection region.
- Result strand - select the DNA strand whose annotations will be considered in the search. If, for example, the "Complement" strand is selected, but all choosen annotations are on the direct strand, than nothing will be found.
- Annotation must fit into region - all annotations, choosen at the left window, must fit completely to the result annotation (completely - and not just in a few characters).
- Save regions as annotations - store results to annotations.
- Clear results - clear the result table.