Results of CAP3 on BAC Data Sets
| Data set | Running time (min) | No. of large contigs | Length of CAP3 sequence | No. of differences[i] |
| 203 | 37 | 1 | 90,292 | 0 |
| 216 | 154 | 1 | 132,057 | 17 |
| 322F16 | 127 | 1 | 157,982 | 11 |
| 526N18 | 73 | 2 | 180,128[ii] | 10 |
[i] The number of differences in highly similar regions of the CAP3 sequence and the provided sequence.
[ii] The sum of the lengths of two large contigs produced by CAP3.