Table 2. Detection probability: RNase T1 unmodified transcript; probability (%) of detecting one SNP in 1000 bp^a.

PCR product size	Forward ww/vvb	Forward ww/wv	Reverse ww/vv	Reverse ww/wv	Forw/Rev ww/vv
1000	25.3	18.0	26.8	18.8	45.8
500	35.6	25.8	35.4	25.8	58.6
333	40.4	29.8	41.2	30.9	65.5
250	44.8	33.6	45.7	35.2	70.9
200	49.0	36.9	49.2	37.3	74.9
100	58.0	45.2	55.8	44.0	82.7

^a10 000 random sequences with 1000 bp containing one random SNP were generated.

^bThe peak pattern of wild-type (w) and variant (v) were simulated and compared in the homozygous (ww/vv) and heterozygous (ww/wv) form. A SNP was detected when at least one difference in the peak patterns was resolved at routine instrument settings. Smaller PCR products were designed with overlapping primer positions so that the entire sequence was covered.