This How-to addresses the problem of finding restriction sites shared by two DNA sequences.

1. Select the first DNA sequence.

2. Click on the main menu Tools > Restriction Enzymes or the contextual menu Sequence Analysis > Restriction Analysis > Restriction enzymes to open the Restriction Enzyme window () if not opened already.

3. Click on the Add Cutters button (). This will select all cutters of the first DNA sequence in the selection panel.

4. If you want only e.g. 6-cutters, select the set of 6-cutters in the restriction enzyme panel and click on the Restrict button (). The selection panel now contain only 6-cutters that all cut the first DNA sequence.

5. Select the second DNA sequence.

6. Click on the All Sites button () in the Restriction Enzyme Window.

7. Open the Output multitab window to access the result.