Table 5.

Discordant TE pairs show higher rates of apparent recombination

	% of pairs w/ evidence of recombination		Mean % id to consensus
	Concordant	Discordant
L1	1.3%	2.8%	79.9%
AluJ	1.6%	5.8%	87.4%
AluS	3.7%	19.0%	93.1%
AluY	5.1%	27.6%	96.2%

For each segmental duplicate TE pair, average segment percent identity was computed over the length of the segment. Then percent identity was computed for non-overlapping length-100 windows for each TE pair. We identified TEs containing windows with significantly reduced identity relative to the containing segmental duplication (P<0.001, Bonferonni correction applied to account for possibly-multiple windows per TE). We quantified the observed rates for Alu and L1 subfamilies, computing apparent recombination in both discordant and concordant pairs