Table 2.

Predicted recombination events determined by different detection methods available in the RDP4 program.

Recombination Event Number	Breakpoint Positions in Alignment		Size (bp)	ORF	Detection Methods
	Begin	End			RDP	GENECONV	Bootscan	Maxchi	Chimaera	SiScan	3Seq
1	67,096	84,072	16,977	075–089	NS	4.95 × 10−35	4.27 × 10−20	2.30 × 10−16	4.98 × 10−17	NS	2.22 × 10−16
2	22 *	4792	4771	001–007	NS	2.01 × 10−18	1.31 × 10−16	2.80 × 10−15	2.80 × 10−15	NS	NS
3	95,124 *	99,574	4451	101–105	NS	1.19 × 10−16	1.13 × 10−16	4.94 × 10−10	4.94 × 10−10	NS	5.24 × 10−14
4	120,668 *	122,753	2086	133	NS	1.95 × 10−17	4.66 × 10−20	8.64 × 10−13	8.64 × 10−13	NS	1.67 × 10−15
5	140,127	144,246	4120	146–149	3.41 × 10−7	7.09 × 10−13	1.97 × 10−9	1.24 × 10−14	1.24 × 10−14	NS	5.55 × 10−15
6	19,579	23,622	4044	027–030	NS	2.54 × 10−14	1.34 × 10−15	1.29 × 10−8	1.29 × 10−8	NS	2.74 × 10−11
7	108,572	111,696 *	3125	116–119	NS	2.01 × 10−11	1.55 × 10−11	6.20 × 10−5	6.20 × 10−5	NS	NS
8	85,944 *	89,483	3540	091–094	NS	2.95 × 10−12	9.72 × 10−11	6.37 × 10−9	6.37 × 10−9	NS	NS
9	45,480	53,842	8363	050–060	NS	1.57 × 10−8	1.35 × 10−5	3.59 × 10−9	3.59 × 10−9	NS	6.29 × 10−12
10	102,225	103,207 *	983	110	NS	2.99 × 10−4	3.01 × 10−5	NS	NS	NS	2.96 × 10−3
11	149,094	151,035 *	1942	154–156	NS	3.17 × 10−4	1.88 × 10−4	NS	NS	NS	NS

* = The actual breakpoint position is undetermined (it was most likely overprinted by a subsequent recombination event).