Table 1. Finding Alu repeats in five sequences.
| Seq | Rep, kb | Family | Alu, bp | Div, % | Sn, % | Sp, % | T, s | Sn,* % | Sp,* % | T,* s |
|---|---|---|---|---|---|---|---|---|---|---|
| 22 Kb | 8 | 10 | 261 (69) | 15.0 (6.4) | 98.4 | 98.9 | 3 | 96.3 | 99.4 | 1 |
| 38 Kb | 13 | 13 | 245 (85) | 15.7 (5.7) | 98.8 | 96.4 | 8 | 98.6 | 96.7 | 4 |
| 167 Kb | 25 | 18 | 261 (72) | 12.2 (5.9) | 95.2 | 93.0 | 44 | 93.5 | 95.2 | 14 |
| 199 Kb | 33 | 13 | 277 (55) | 15.0 (5.6) | 99.3 | 92.6 | 62 | 85.2 | 93.7 | 32 |
| 1 Mb | 85 | 32 | 252 (79) | 15.2 (6.1) | 95.3 | 98.9 | 293 | 72.4 | 99.4 | 85 |
Seq, sequence length; Rep, total length of Alus marked by repeatmasker; Family, no. of Alu subfamilies; Alu, average Alu size with SD shown in parentheses; Div, average divergence from the closest subfamily's consensus with SD shown in parentheses. All SDs were computed by excluding repeats from LTRs, 7 SLRNA, and SVA subfamilies. Sn, sensitivity; Sp, specificity; T, computation time.
*
Indicates results by a fast version of our program. The computation time was greatly reduced, but the last two cases also show reduced sensitivities