Table 6 |
||||
| Balancing cross hybridization, sliding and hairpins | ||||
| No. | ΔG | SHINet al. | ΔG | FELDKAMP |
 |
5’ → 3’ |  |
5’ → 3’ | |
| 1 | 0.8 | AGGCGAGTATGGGGTATATC | 1.0 | TAGTCGCGTGATTTGGAAGG |
| 2 | 0.8 | TTATGATTCCACTGGCGCTC | 0.6 | TTACACTTGAAGCTGGCTCG |
| 3 | 0.3 | CTTCGCTGCTGATAACCTCA | 0.3 | CTTCGTGTCGGCCATCATAT |
| 4 | 0.2 | CGCTCCATCCTTGATCGTTT | -0.2 | AAAGCCGTCGTTTAAGGAGC |
| 5 | 0.1 | ATCGTACTCATGGTCCCTAC | -0.3 | GGTTCTTACGCTCTACTGCA |
| 6 | -0.3 | GAGTTAGATGTCACGTCACG | -0.6 | TACGTCTCGAACTGATAGCG |
| 7 | -2.3 | CCTGTCAACATTGACGCTCA | -2.4 | TCATGTTGGCACCGTATGCA |
| # | ||||
| Lc | 6 | 5 | ||
| Lhp | 6 | 4 | ||
| Lsc | 6 | 6 | ||
| Lsl | 7 | 4 | ||
| No. | ΔG | EGNAS | ΔG | EGNAS |
 |
First set |  |
Second set | |
| 5’ → 3’ | 5’ → 3’ | |||
| 1 | * | CAAAGAACCGACATAGCCAC | * | CCAACCAAACCACCAATCTC |
| 2 | * | GAACGGCAGGAGACAAATAC | 1.4 | CTGTCGTCGTGTCTTCTTCA |
| 3 | * | CATAAGAGGAAACAGCACGG | 1.3 | GCAGGCAGGTCAAGGTAAAT |
| 4 | 2.1 | GTTCGTCCTATTGCTCTGTG | 1.0 | ATCCGCCATAATAAGTCCGC |
| 5 | 1.5 | GTCGTGTTGCCTTTCTATCC | 0.9 | CTTTCGGCTCCTAACATTCG |
| 6 | 1.3 | GGTTTATTCTCGGCTTGTGG | 0.7 | GAGTGAGTTCCAGAGTATCG |
| 7 | 1.3 | GGCTCGTTTGGTGTATCTTC | 0.5 | TTGTAGCATCATCAGCGAGG |
| GC ends | ||||
| # | # | |||
| Lc | 5 | 4 | ||
| Lhp | 2 | 3 | ||
| Lsc | 4 | 4 | ||
| Lsl | 3 | 6 | ||
Comparison of 20 bases long sequences generated by SHIN et al. [16], FELDKAMP et al. [20] and EGNAS. Molar free enthalpies of the most stable hairpins.
*No hairpin structure possible.
#Without {GGG;CCC;AAAA;TTTT}.
Kick et al. BMC Bioinformatics 2012 13:138 doi:10.1186/1471-2105-13-138
