#CRISPR genomic target structure clarified here in my blog post. Target = protospacer + PAM.

When discussing CRISPR "targets", it's important to use precise terms to describe the important features.    The genomic target of CRISPR-Cas9 is composed of two parts: (1) the protospacer and (2) the protospacer-adjacent-motif, or PAM.

Note that the PAM does not base-pair with the CRISPR/guide RNA at all.   It appears to interact with the Cas9 protein directly.  The CRISPR RNA only base pairs with the DNA base that are complementary to the protospacer.   

It's wise not to use "target" and "protospacer" interchangeably in CRISPR-related discourse; it causes headaches at the design stage.  Bottom line: screen your genomic sequences of interest for occurrences of the full target, but only the protospacer (not the PAM) becomes part of the CRISPR/guide RNA.