There is a new feature accessed by the Analyze | CRISPR PAM sites... menu item that will scan Nucleic Acid sequences for Protospacer Adjacent Motifs associated with the CRISPR Cas9 and related enzymes cleavage and modification functions. By default, MacVector uses a file called Protospacer Adjacent Motifs.pam that is located in the /Applications/MacVector/Subsequences/ folder. It contains most of the current (July 2020) characterized Cas9-like enzymes, but you can always open the file and add your own.
While MacVector does not search genomes for potential off-target sites (see below), this is still a very useful function to alert you to potential CRISPR target sites. The output is a mix between the current Restriction Enzyme and Nucleic Acid Subsequence searches, so you can easily see and copy the guide sequences.
You can also have MacVector automatically scan for CRISPR PAM sites whenever you open a DNA sequence file. MacVector will automatically scan DNA sequences for various features whenever you open a sequence. To control what is shown go to EDIT | SCAN DNA. All displayed features can be easily directly annotated by right clicking or double clicking to open in the Symbol editor
The scoring is based on this paper:
Note that the score is only relevant to the likelihood that a guide RNA targeted at that site will actually be recognized and act as a cleavage for the enzyme. All scoring systems were trained on the standard SpCas9 system and are likely not relevant for other systems. In particular, note that this is a purely "local" scoring system - it does not take into account other potential off-targets in whatever genome you are using. For that you would need to download your genome and run a Primer Database Search against it using your guide RNA as a "primer".