| Tools | Family | Total Size (Kb) | Family Accuracy | Size Accuracy | Repeat Accuracy | Copy Accuracy | Location Error |
| HashRepAligner | 24 | 8.56 | 95.8% | 93.21% | 95.45% | 92.1% | 3.21% |
| Bowtie | 20 | 7.32 | 86.9% | 91.51% | 86.31% | NA | 6.78% |
| Soap | 26 | 12.89 | 86.7% | 83.87% | 87.64% | NA | 8.96% |