Highest Scoring Nontrivial Patterns with (at Most) One Wild-Card Symbol
| No.[ii] | Pattern | Score[iii] | N+[iv] | N−[v] |
| A. Regions −100..0 | ||||
| 2 | AAG.AAACAAA | 6.54 | 37 | 1 |
| 6 | A.TAAGAACA | 5.79 | 27 | 0 |
| 8 | A.AATAGGA | 5.61 | 43 | 3 |
| 9 | AAGAAA.CAAA | 5.58 | 26 | 0 |
| 12 | GTAACAA.C | 5.36 | 25 | 0 |
| 13 | AAA.AACTTA | 5.36 | 25 | 0 |
| 20 | ACAAC.TAA | 5.09 | 39 | 3 |
| 21 | AG.AAACAAA | 5.06 | 64 | 8 |
| 23 | ACAAACAA.A | 4.97 | 48 | 5 |
| 26 | AATAGTA.A | 4.92 | 77 | 11 |
| 32 | AATAGTATA | 4.77 | 27 | 1 |
| 34 | TCACTAC.T | 4.72 | 22 | 0 |
| 35 | CAAACA.ACA | 4.72 | 22 | 0 |
| 37 | ACA.ATAGA | 4.72 | 55 | 7 |
| 42 | AGAGA.ATA | 4.63 | 54 | 7 |
| 47 | AATAAACAA.A | 4.59 | 26 | 1 |
| 50 | AAAG.ACAAG | 4.57 | 35 | 3 |
| 52 | CTAAGAA.A | 4.55 | 53 | 7 |
| 56 | A.AAGGGAAG | 4.51 | 21 | 0 |
| 57 | CAAA.TAAC | 4.50 | 48 | 6 |
| B. Regions −250..−150 | ||||
| 14 | TTACCCGC | 6.22 | 29 | 0 |
| 58 | GT.ACCCG | 5.59 | 54 | 5 |
| 71 | T.ACCCGC | 5.48 | 42 | 3 |
| 126 | CGGGTA.T | 5.06 | 64 | 8 |
| 141 | G.TACCCG | 4.97 | 48 | 5 |
| 165 | CGGGTAA.A | 4.87 | 47 | 5 |
| 178 | GTTACCCG | 4.83 | 37 | 3 |
| 305 | TACAT.TATA | 4.43 | 65 | 10 |
| 353 | TTTCTC.TTT | 4.32 | 46 | 6 |
| 372 | TTACCCG | 4.30 | 119 | 23 |
| 379 | TTTCCTGT.T | 4.29 | 20 | 0 |
| 405 | CTCATCTC.T | 4.24 | 24 | 1 |
| 425 | TCACGTGA | 4.20 | 28 | 2 |
| 427 | T.ATATATTC | 4.20 | 28 | 2 |
| 454 | CGGGTAA | 4.12 | 114 | 23 |
| 460 | TGTGT.GAT | 4.08 | 19 | 0 |
| 465 | ATTACCCG.A | 4.08 | 19 | 0 |
| 474 | G.ACATATAT | 4.06 | 23 | 1 |
| 485 | TA.GTAAAC | 4.05 | 27 | 2 |
| 500 | TTTCTCT.TT | 4.03 | 47 | 7 |
[i] Matches were only allowed on the W (gene) strand.
[ii] No. of the pattern enumerating them decreasingly by scores (before trivial patterns were removed).
[iii] From equation 2.
[iv] No. of upstream regions matching the pattern.
[v] No. of random sequences matching the pattern.