Table 1.

Coverage by Outer Alignments

Score	1 Mus	>1 Mus	1 Rev	>1 Rev
3000	0.36814	0.02340	0.00084	0.00080
4000	0.36859	0.02230	0.00040	0.00074
5000	0.36958	0.01975	0.00016	0.00059
6000	0.36992	0.01829	0.00013	0.00051
7000	0.36997	0.01697	0.00011	0.00043
8000	0.36966	0.01586	0.00010	0.00037
9000	0.36911	0.01490	0.00008	0.00033
10000	0.36831	0.01405	0.00007	0.00030

The columns have the following meanings: (1) score threshold for a gapped outer alignment (Step 2.2.2 of Fig. 1); (2) fraction of the genome covered by exactly one alignment; (3) fraction of the genome covered by more than one alignment; (4) fraction of the genome covered by exactly one alignment with reversed mouse; (5) fraction of the genome covered by more than one alignment with reversed mouse.