TABLE 2.

Comparison of recombination breakpoints determined by HIVE-hexahedron and Geneious-derived sequences^a

Virus	HIVE-hexahedron		Geneious
	Region	Subtype	Region	Subtype
707010585	4906–6541	C	4906–6425	C
	6542–8080	A1	6426–8059	A1
	8081–9531	C	8060–9411	C
707010134	4906–8321	C	4906–8274	C
	8322–8864	D	8275–8764	D
	8865–9621	C	8765–9392	C
PK-011	4906–8777	CRF02_AG	4906–8760	CRF02_AG
	8778–9591	A1	8761–9603	A1
PK003	4932–8920	CRF02_AG	4906–8784	CRF02_AG
	8921–9624	A1	8785–9606	A1
PK033	4906–6037	CRF02_AG	4906–6162	CRF02_AG
	6038–9608	A1	6163–9606	A1
PK008	4906–6033	A1	4906–6056	A1
	6034–7398	CRF02_AG	6056–7680	CRF02_AG
	7399–8067	A1	7681–7929	A1
	8068–8388	CRF02_AG	7930–8330	CRF02_AG
	8389–9238	A1	8331–9279	A1
	9239–9624	CRF02_AG	9280–9604	CRF02_AG
PK015	4904–6243	CRF02_AG	4906–6127	CRF02_AG
	6244–9611	A1	6128–9606	A1
707010277	4906–7025	C	4906–7072	C
	7026–8457	A1	7073–8365	A1
	8458–8776	C	8366–8672	C
	8777–9587	A1	8673–9526	A1
PK023	4907–6256	CRF02_AG	4906–6154	CRF02_AG
	6257–6473	A1	6155–6553	A1
	6474–8846	CRF02_AG	6554–8801	CRF02_AG
	8847–9624	A1	8802–9605	A1
PK006	4905–6252	CRF02_AG	4906–6192	CRF02_AG
	6253–7577	A1	6193–7516	A1
	7578–8474	CRF02_AG	7577–7876	CRF02_AG
	8475–8852	A1	7877–8176	A1
			8177–8965	CRF02_AG
	8853–9624	CRF02_AG	8966–9606	A1

^aThe shaded cells represent conflicting recombination patterns between Geneious and HIVE-derived sequences (Fig. S3).