Table 1 Detected target site duplication (TSD) position and sequences.

Chromosome	Position	TSD sequence	VnP1	VnP2	VnP3	Gene in the flanking region
nrPERV confirmed with both 5′- and 3′-TSD
SSC 1	38,667,241	CTAT	LTR	LTR	LTR	NKAIN2
SSC 1	256,173,876	CCCC	PERV-B	PERV-B	LTR	ENSSSCG00000046664
SSC 1	259,647,577	AATC	LTR	LTR	LTR	N/A
SSC 2	3,400,723	AGAAC	PERV-B	LTR	LTR	N/A
SSC 4	77,324,504	CCCC	LTR	LTR	LTR	N/A
SSC 4	78,524,842	ATTAC	LTR	LTR	LTR	SNTG1^a
SSC 4	121,221,912	GGGG	LTR	LTR	non-LTR	N/A
SSC 6	73,460,691	GTAT	LTR	LTR	LTR	KAZN
SSC 8	137,488,280	CTAT	LTR	LTR	LTR	CFAP299
SSC 9	61,533,579	GGTG	LTR	LTR	non-LTR	N/A
SSC 9	76,895,449	GAAC	PERV-B	PERV-B	PERV-B	N/A
SSC 9	135,717,008	AAGAG	LTR	LTR	LTR	N/A
SSC 12	60,076,460	CTGCT	PERV-B	PERV-B	PERV-B	LOC110256117
SSC 13	57,502,585	TAAA	LTR	LTR	LTR	N/A
SSC 13	60,210,737	GTAG	LTR	LTR	non-LTR	LOC106505659^c
SSC 13	73,434,304	TTAT	LTR	LTR	non-LTR	N/A
SSC 14	4,896,607	AGGGT	LTR	LTR	non-LTR	N/A
SSC 14	27,599,572	ATGC	PERV-B	PERV-B	LTR	N/A
SSC X	70,665,683	ATAT	PERV-B	PERV-B	PERV-B	LOC102165634
SSC X	75,151,968	CCAG	PERV-B	PERV-B	PERV-B	PCDH11X
SSC X	119,479,008	AATT	LTR	LTR	non-LTR	N/A
nrPERV confirmed with either 5′- or 3′-TSD
SSC 8	51,601,922	ATGA	PERV-C	PERV-C	PERV-C	LOC106504658^b
SSC 8	137,628,915	ATGAC	non-LTR	non-LTR	LTR	ANTXR2
SSC 13	107,045,657	ATTC	PERV-A	non-LTR	non-LTR	LOC100153543
SSC 14	8,846,347	GAGG	LTR	LTR	non-LTR	N/A
SSC 18	4,030,456	ATGT	non-LTR	non-LTR	non-LTR	N/A

Chromosome number and position are based on the Sscrofa11.1 reference genome. Gene symbols are as follows: NKAIN2, Na + /K + transporting ATPase interacting 2; ENSSSCG00000046664, lncRNA; SNTG1, syntrophin gamma 1; KAZN, kazrin, periplakin interacting protein; CFAP299, cilia and flagella associated protein 299; ANTXR2, anthrax toxin receptor 2; LOC110256117; mRNA-multidrug and toxin extrusion protein 1-like, transcript variant; LOC100153543, multiple epidermal growth factor-like domains protein 10-like (predicted); PCDH11X, protocadherin 11 X-linked. LOC102165634, LOC106504658, and LOC106505659 are uncharacterized genes. N/A, not applicable.
^aTSD position is 2.5 kb downstream of the gene.
^bTSD position is 25 kb downstream of the gene.
^cTSD position is 16 kb downstream of the gene.

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