Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse

Table 2 Maximum match between polytropic murine leukemia retrovirus (Mpmv) and each next generation sequenced MLV region, in 5 mice

Reference	MLV region	C3H	LP/J	SJL	Mmd1	Mmd2
Mpmv1	1	99.8	100	99.5	99.3	99.5
	2,3	99.7	100	99.7	99.7	100
	5	100	100	100	99.7	100
	6	99.5	100	99.8	99.3	100
Mpmv2	1	99.8	99	98.8	98.6	100
	2,3	100	100	99.5	99.5	100
	5	100	100	100	99.7	100
	6	100	99.8	99.5	99.5	99.8
Mpmv4	1	100	99.8	99.8	99.5	100
	2,3	100	99.7	99.5	99.5	99.7
	5	100	99.7	99.7	99.5	100
	6	100	100	100	100	100
Mpmv5	1	99.5	99.3	99.3	99	99.3
	2,3	98.9	98.9	98.9	98.7	99.2
	5	99.7	99.7	99.7	99.5	99.7
	6	99.3	99.3	99.3	99.3	99.3
Mpmv6	1	100	100	99.3	98.8	99.3
	2,3	100	100	99.5	99.5	99.7
	5	100	100	99.7	99.7	99.7
	6	99.8	99.3	98.6	98.6	98.8
Mpmv7	1	99.5	100	99	98.8	99.8
	2,3	100	100	99.7	99.7	100
	5	100	100	100	99.7	100
	6	100	100	99.8	99.8	100
Mpmv8	1	99.3	99	99	98.8	99.3
	2,3	100	99.7	99.5	99.2	99.5
	5	100	99.7	99.7	99.5	100
	6	100	100	100	100	100
Mpmv9	1	99.8	99	98.8	98.6	100
	2,3	100	100	99.5	99.5	100
	5	100	100	100	99.7	100
	6	100	99.8	99.8	99.8	100
Mpmv10	1	100	100	99.5	99.3	99.5
	2,3	100	100	99.5	99.5	99.7
	5	-	-	-	-	-
	6	100	100	99.5	99	99.3
Mpmv11	1	100	100	100	99.8	100
	2,3	100	100	99.7	99.7	100
	5	99.7	99.7	99.7	99.5	99.7
	6	99.5	99.5	99.5	99.5	99.5
Mpmv12	1	100	99.3	99	98.8	99.8
	2,3	100	99.7	99.5	99.2	99.7
	5	100	100	100	99.7	100
	6	99.8	99.5	99.5	99.5	99.5
Mpmv13	1	99.8	99.8	99.8	99.5	99.8
	2,3	99.5	99.5	99.5	99.2	99.7
	5	99.5	99.5	99.5	99.2	100
	6	100	100	100	100	100

The use of boldface indicates that sequences with 100% identity to a reference were detected for all MLV target regions in a mouse. The use of italics indicates that more than one Mpmv sequence in a cluster was 100% identical. Mpmv reference sequences are those of Bamunusinghe et al. [4]. A dash indicates that for a target MLV region, the region is deleted in the reference sequence relative to other MLV sequences