Table 1.
Sequence-level comparisons cannot faithfully predict thermodynamic properties
| Probe (top strand) and nontarget (lower strand) match (complementary bases in uppercase; mismatched bases in lowercase) | Nontarget match identity (bp) | Nontarget match stretch (bp) | Probe to nontarget melting temp. (°C) | Probe to target melting temp. (°C) |
|---|---|---|---|---|
| tagagtagAAaaaCAAataAaAGAcattaaAGAAAATGATTTTTgattTttgtgttagTTaccGTTacgTgTCTcacgccTCTTTTACTAAAAAaagtAt | 24 | 14 | 28.39 | 55.14 |
| CTtgAaaTtgaaTacAaattctaTaaaTCAATGATATGAATacaataACAGAtgTggAtagaAgcTacctcgaAgggAGTTACTATACTTActcaccTGT | 24 | 14 | 29.92 | 54.33 |
| TcaAAgtctAtgatAttcgacAtAtaaTctTGAATCGAAAAAACaGCctcAagTTtctcTtaccTgtctgaTgTtgaAatACTTAGCTTTTTTGaCGcct | 24 | 14 | 38.04 | 61.27 |
| cGGTGCTCGATACGAttGCcCtgatgcTGacaaggCttctaTcgAaTCtcaCCACGAGCTATGCTctCGaGggccacACaagcggGttccgAagTaAGga | 24 | 14 | 48.01 | 72.36 |
| agcagTcgCtAcCGcttgcCGGACGAATTGCCGgTCGctccTgtttGggcctaaaAaaGcTcGCattttGCCTGCTTAACGGCaAGCacaaAaggcCttt | 24 | 14 | 58.02 | 80.75 |
| AacGgAGAaggaGagTgCcgggcGGAAGCCGGCGGCGaaaaCgTccaccgTgcCgTCTaggaCatAgGcttacCCTTCGGCCGCCGCacggGtActgcta | 24 | 14 | 64.30 | 82.65 |
| gGCCGGTGGCGGCCGtGagatgtcgctctCggcGAatgGCatTctgAtCTaCGGCCACCGCCGGCtCaaatgttatctcGgaaCTacaCGctAcggTgGA | 24 | 14 | 68.56 | 80.10 |