Table 1. Base pair distance between the sampled and native structures for cis-regulatory elements from Hepatitis C virus and HIV.
| RNA | #seq | length | #bp | 0 | 1 | 2 | 3 | 4 | 5 |
| HCV CRE | 52 | 51.0 | 14 | 1.8/0 | 2.7/0 | 6.1/2 | 8.6/1 | 10.8/9 | 12.4/10 |
| HCV SLIV | 110 | 35.0 | 15 | 0.3/2 | 0.3/1 | 0.3/1 | 0.3/1 | 0.3/1 | 0.3/1 |
| HIV PBS | 388 | 94.8 | 17 | 12.3/4 | 14.9/5 | 16.7/1 | 17.6/1 | 18.3/1 | - |
| HIV FE | 853 | 51.9 | 10 | 7.6/1 | 7.7/2 | 7.7/2 | 7.6/2 | 7.4/2 | 7.2/2 |
| HIV GSL3 | 1403 | 81.1 | 8 | 9.3/0 | 9.1/0 | 8.9/0 | 9.2/0 | 9.6/0 | - |
Native structure is here taken as the Rfam consensus structure from the seed alignments of these elements of HCV and HIV. Two measures are given. The average distance represents the average base pair distance between sampled structures and the native secondary structure S 0. The centroid represents the average base pair distance between sampled structures and the sample centroid S c, where the latter is defined to consist of those base pairs occurring in strictly more than half the sampled structures. The number of sequences in the Rfam seed alignment, the average length and the number of basepairs in the native structure are given before the average and centroid distance values.