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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

[i] 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.