Table II. Comparison of predicted motifs with known plant motifs.
The comparisons are based on 8-mers. The comparison becomes unnecessary when the mismatch number α is larger than 1, since 84.5% of 8-mer segments in C. reinhardtii will be defined as conserved 8-mers by the mismatch number-counting method when α = 2.
| Method | E Value Cutoff |
||
|---|---|---|---|
| 1E-5 | 1E-6 | 1E-7 | |
| MERCED | 195 (62%) | 112 (35%) | 72 (23%) |
| α = 0 | 171 (54%) | 103 (32.5%) | 52 (16.4%) |
| α = 1 | 179 (56.5%) | 100 (31.5%) | 57 (18.0%) |
| FastCompare | 169 (53.3%) | 97 (30.6%) | 50 (15.8%) |
| PhyloNet | 188 (59.3%) | 104 (32.8%) | 33 (10.4%) |