Table 1.
Comparison of BLASTN and WABA Alignments
| BLASTN default | BLASTN −W8−f8 | WABA | |
| Total base matches | 1849727 | 1969827 | 4697347 |
| Total base mismatches | 314023 | 340606 | 2538033 |
| Total bases inserted | 5859 | 5659 | 2275269 |
| Total number of inserts | 2836 | 2962 | 27469 |
| Number of alignments | 14653 | 16247 | 3839 |
| Average size of alignments | 147.9 | 142.4 | 2059.3 |
| C. briggsaecosmids total | 229 | 229 | 229 |
| Cosmids with any alignment | 224 | 224 | 227 |
| Seconds to align one cosmid | 60 | 2461 | 1420 |
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Only alignments containing 50 or more base matches are included here. BLASTN was run at the default settings and with the window size and the minimum extension score set down to eight for increased sensitivity. WABA is more tolerant of long inserts and nucleotide mismatches than BLASTN at either setting and consequently is able to make longer alignments.
