Example of showing potential cuts at ambiguous bases

The following example shows the use of the Show Potential Cuts at Ambiguous Bases option, located in the Enzymes panel:

1. Create a new DNA project and paste in the following sequence, which contains many ambiguous bases:

ATGWSNGCNAARGCNGARAGGATCCARAARCCNGCNWSNAARGCNCCNGCNGARAARAARCCNGCN

Several enzymes are applied to the sequence automatically and are visible in the Sequence view.

2. From the Enzymes panel, check the box next to AluI, which has the recognition sequence AGCT.

There are two possible outcomes, depending on whether Show Potential Cuts at Ambiguous Bases is checked or unchecked in that panel:

• • Unchecked (default): Since the literal sequence AGCT is not present in the DNA sequence, no AluI enzymes appear on the sequence.
    
    
  • Checked: Even though AGCT is not present, RGCN and NGCN are both recognized as potential sites, and the enzyme AluI appears in six locations on the sequence.
    
    ATGWSAA(RGCN)GARAGGATCCARAARCCWSNAACC(NGCN)GARAARAARCC