Table 3.
Estimated frequency of intron-flanking repeats as large or larger than observed in the natural data under species-specific random models of ciliate genes.
| Assumed intron splicing constraints | ||||
| Species | intron | None† | Eukaryotic‡ | Ciliate§ |
| Holosticha | 1 | 42** | 2076+ | 4801~ |
| Uroleptus | 1 | 60** | 2409+ | 5849~ |
| Sterkiella | 1 | 148** | 6848 | 14413 |
| Paraurostyla | 1|| | 8129 | 72072 | 72072 |
| Stylonychia | 1|| | 7636 | 73737 | 737373 |
| Eschaneustyla | 1|| | 5928 | 81905 | 81905 |
| Holosticha | 2 | 709 | 408+ | 2583~ |
| Uroleptus | 2|| | 11191 | 17469 | 100000 |
| Paraurostyla | 2|| | 1415 | 26895 | 58273 |
| Stylonychia | 2|| | 12891 | 12891 | 27924 |
| Sterkiella | 2|| | 10739 | 10739 | 19570 |
| Urostyla | 1 | 4** | 2+ | 0~ |
| Uroleptus | 3 | 19** | 6895 | 42397 |
| Eschaneustyla | 2|| | 314** | 81905 | 81905 |
** FDR ≤ 0.01, + FDR ≤ 0.1, ~FDR ≤ 0.25: FDR (False Discovery Rate) controlled within each column by the method of Benjamini and Hochberg (1995), which was shown to control the FDR for positively dependent test statistics by Benjamini and Yekutieli (2001).
† No intron splicing constraints: the entire intron was permuted.
‡ Eukaryotic intron splicing constraints: the two bases at the 5' and 3' intron ends were fixed.
§ Putative ciliate intron splicing constraints: the five 5'-most and three 3'-most bases of the introns were fixed.
|| The values in italics were calculated exactly, multiplied by 105 and rounded; other values in upright face were calculated from permutation tests (N = 100,000).