Table 2.

Annotation of TE pairs in segmental duplications, for the three types of Alu subfamilies

	Concordant	Non-match	Non-match	Non-match	Other, e.g.	Mismatch
		AluJ	AluS	AluY	FRAM/FLAM	percent
AluJ	2308	254	69	10	134	16.8%
AluS	5776	69	629	77	24	12.2%
AluY	973	10	77	89	4	15.5%

In this table, each cell tallies the number of cases where one of the elements of a segmental duplicate TE pair belongs to the type specified by the row (from among AluJ, AluS, and AluY), and the other element belongs to type specified by the column. The first column captures concordant pairs (both entries share the same subfamily). In the next three columns, a cell captures the count of cases where one element belongs to one subfamily (specified by row), and the other element belongs to a different subfamily, and belongs to the type specified by the column (e.g. there are 254 cases in which an AluJ type instance is paired with another instance with a different subfamily that is still of the AluJ type; meanwhile there are 69 cases in which an AluJ type is paired with an AluS type). Mismatch percents (final column) exceed those in the previous table, because each discordant pair is double counted. The table is intended to highlight the differences in between-type discordance rates