Table 4.

Percentage of Bases of Mouse LINE-1 Subfamilies That Match Mouse piRNAs

	Subfamily	0 Mismatch, %	1 Mismatch, %	2 Mismatch, %
Inactive	L1MdF	1.73	6	13.2
	L1MdF2	4.6	15.1	21.8
	L1MdF3	4.85	14.2	21.6
Active	L1MdGf	5.8	16.8	22.52
	L1MdT	10.3	18.9	26.5
	L1MdA	9.45	17.5	24.0

Repeat Masker (http://www.repeatmasker.org) annotates the six youngest LINE-1 subfamilies in the mouse genome (UCSC genome version mm9) as L1MdF, L1MdF2, L1MdF3, L1MdT, L1MdGf, and L1MdA. The different F-subfamilies annotated as L1MdF, L1MdF2 and, L1MdF3 summarize a more complex phylogeny of up to 17 subfamilies of mouse-specific LINE-1s. LINE-1 elements belonging to the subfamilies L1MdT, L1MdGf, and L1MdA have been reported to be currently active (Naas et al. 1998; Hardies et al. 2000; Goodier et al. 2001).