Hello! Thank you for your request!

To manually distinguish the pattern annotations you can do the following:
1) Look at the Sequence Zoom View and pay attention to the regions where CDS annotations are located - see the screenshot.
2) Move all annotation into one folder and sort them by the location value. Then, go through the annotations and manually move the required intersected annotations into another folder.

Alos, you might like to participate in a UGENE webinar. In this case I will show you these features in details and other useful features as well.

I've also created an issue in our tracker system (UGENE-3703) to automate the described procedure with the workflow sample .

Ilya, I've create UGENE-3808 for your request.

Ilya, full bedtools support is actually a good idea. But I think that in the workflow designer it wouldn't be that interesting as it was integrated in the sequence view. I mean it would be much more convenient (for manual analysis) to perform those overlaps/coverage operation for selected annotations in the sequence view. We should think about how to do it nice.

Ilya, actually you can run any program or script in the WD by creating a custom element. Have you tried this feature?

Note that if it is a script, you should specify the corresponding script interpreter executable file while creating the element, for example, the execution string will be "python myScript myScriptParams".