Tentative and clear recombination sites in Cauliflower mosaic virus genomes.

aRecombination sites detected in the CaMV genomes by the recombination detection programs (listed in column 6), from the aligned sequences of the likely recombinant and its ‘parental isolates’. The nucleotide position shows locations of individual genes numbered as in Xinjing genome (AF140604). UD; Undetermined.bRecombinant isolates identified by the recombination detection programs: R (RDP), G (GENECONV), B (BOOTSCAN), M (MAXCHI), C (CHIMAERA) and SR (SISCAN) programs in RDP4, and SO (SISCAN total nucleotide site analysis) in original SISCAN version 2 and P (PHYLPRO) programs. The analyses were done using default settings and a Bonferroni-corrected P-value cut-off of 0.01 in RDP4.cThe reported P-value is for the program in bold type and underlined in RDP4 and is the smallest P-value among the isolates calculated for the region in question. P-values smaller than 1.0×10−5 are listed.