We messed around with bowtie - it seems like most of these are optimized for the number of alignments being small (i.e. close to 1). Unfortunately, the number

We messed around with bowtie - it seems like most of these are optimized for the number of alignments being small (i.e. close to 1). Unfortunately, the number of matches for a 20 base guide on the human genome is closer to 1000.