I designed a bait set to caputure genes but i would like to know whether my baits bind on other places other than the designed gene sequences. My idea is to blast it back to the reference genome and identify the "background noise" of the non gene sequences. An easy solution i think is to remove all gene sequences from my reference genome. Leaving only the intergenic and repetitive regions. 

Does someone have a easy solution for this?
Or other suggestion i could try? 
get a BED for your genes and then use bedtools mask fasta http://bedtools.readthedocs.io/en/latest/content/tools/maskfasta.html to replace the bases with N.