. 2012 Jun 5;4(6):940–953. doi: 10.3390/v4060940

Table 1.

Tomato chlorotic dwarf viroid (TCDVd) sequence variant population structure, occurrence frequency and nucleotide variation in TCDVd isolate Trust-infected tomato plants.

Sequence variant	Size (nt)	Occurrence frequency (%)		Nucleotide difference from the reference sequence ^a
Sequence variant	Size (nt)	Plant 1	Plant 2	Nucleotide difference from the reference sequence ^a
AF162131	360	n/a	n/a	n/a
I	360	66.7	65.7	No variation
II	360	33.3	28.6	178 (U to A); 182 (C to U); 183 (A to U)
III	360	0	2.9	165 (U to C)
IV	360	0	2.9	149 (A to G)
Haplotype diversity ^b		0.500 ± 0.128	0.499 ± 0.071
Nucleotide diversity ^c		0.00417 ± 0.00107	0.00382 ± 0.00057

^a AF162131 was used as a reference sequence. Nucleotide differences in each variant were indicated in relation to the reference sequence at positions in the reference; ^b/c Haplotype and nucleotide diversities were calculated using the software DnaSP v5; n/a: not applicable.