Table 3. Secondary structure and repetitive elements in the edited regions.
| Property | Ultra-editingc , d | DARNED short clustersc , d | P-valuee | |
| 1 | Maximum length of dsRNA using BLASTa. | 322±11 | 212±4 | 9.6×10−23 |
| 2 | Maximum length of dsRNA using RNA Foldb. | 400±5 | 363±2 | 2×10−12 |
| 3 | Total repeat content in the region. | 63.2%±0.7% | 52.6%±0.3% | 6×10−37 |
| 4 | Minimum of (number of +Alus, number of −Alus) in the region. | 3.8±0.09 | 3.59±0.04 | 2.6×10−2 |
| 5 | Distance between the edited Alu and the nearest inverted Alu. | 855±52 | 956±21 | 3.4×10−7 |
a
The edited region and its reverse complement were aligned using BLAST. We used the total number of aligning base pairs as an estimate of the length of the dsRNA.
b
The secondary structure of the RNA was calculated using RNAFold [50]. We used the maximal number of open brackets in the structure as an estimate of the length of the dsRNA.
c
Regions used: 1.5 kbp flanking upstream and downstream of the edited regions for properties 1,2, and 3; 5 kbp for property 4.
d
Means are reported along with the standard error of the mean [sqrt(sample variance/n)].
e
P-values were calculated using Mann-Whitney U test.