Using Bowtie (for example v1.2.2 here) to find off-targets for defined CRISPR-Cas9 target sequences:
Make the Bowtie index for your genome (fasta file format)
bowtie-build -f genome.fa genome_prefix
Search for your target sequence by allowing 1 mismatch (for your N) with the flag
bowtie genome_prefix -n 1 -c GGAGCGAGCGGAGCGGTACANGG
It should find back your origin sequence even with 1 mismatch (your N in this case). To allow 2 mismatches, use
-n 2. Even though up to 3 mismatches are allowed with the
-n argument, only 2 mismatches will be tolerated (I wrote an issue in their GitHub repository). The seed length is 28 by default so you don't need to change that as you work with CRISPR-Cas9 target sequences (typically 20 bp). Check more in Bowtie documentation.
Note: I use Bowtie since Bowtie2 allows maximum 1 mismatch, which is a drawback in this case. Note also that while you can search for a sequence containing Ns, Bowtie does not allow alignment to Ns contained in your reference genome (but bowtie2 does). I think it would be nice to have the flexibility of Bowtie regarding the number of mismatches allowed and the ability of Bowtie2 to align to sequences containing Ns. Despite this, Bowtie is used to identify off-targets in the most common webtools for sgRNAs design such as CHOPCHOP or CCTop.