Table 1. Mu-seq library alignment statistics.

	Reads	% of total reads
Total trimmed reads1	90,884,507
aligned reads1	88,364,143	97.2
accepted alignments	87,269,249	96.0
rejected alignments: >4 copies2	662,509	0.7
rejected alignments: start site3	432,385	0.5

¹Mu-seq reads were trimmed and aligned to the maize genome as described in Materials and Methods.

²Alignments that matched more than four sites in the genome with equivalent scores were excluded.

³Alignments that did not begin within 10 bases of the 5-prime end of the read were excluded.