Table 1.

Summary statistics for true alignments on 1,000-sequence data

		p-distance		Gaps/Seq	Gap Length	% Blank
	Sites	Avg	Max
RNAsim	4806	41 %	61 %	1036	3.1	68 %
Indel. M2	2179	67 %	74 %	210	5.6	54 %
Rose L1	3777	70 %	77 %	209	13.2	73 %
Rose M1	3934	70 %	77 %	294	9.9	74 %
Rose S1	2106	69 %	77 %	285	3.9	52 %

The p-distance is the normalized pairwise Hamming distance. Numbers shown are averages over 10 replicates