TABLE 4.
Similarity analyses of the root area of potential hairpin structure.
|
LCS |
LCSeq |
Levenshtein distance |
Hamming distance |
|||||||||||||
| 10 bp | 20 bp | 30 bp | 100 bp | 10 bp | 20 bp | 30 bp | 100 bp | 10 bp | 20 bp | 30 bp | 100 bp | 10 bp | 20 bp | 30 bp | 100 bp | |
| D2 | 2 | 6 | 7 | 7 | 4 | 10 | 18 | 64 | 7 | 13 | 16 | 52 | 7 | 15 | 18 | 63 |
| D6 | 5 | 5 | 5 | 6 | 7 | 13 | 20 | 59 | 5 | 9 | 14 | 60 | 7 | 13 | 20 | 64 |
| D7 | 2 | 5 | 5 | 8 | 5 | 10 | 18 | 66 | 6 | 12 | 16 | 50 | 6 | 12 | 21 | 68 |
| D8 | 4 | 5 | 5 | 6 | 5 | 10 | 17 | 64 | 7 | 14 | 19 | 53 | 7 | 15 | 21 | 72 |
| D9 | 2 | 4 | 5 | 5 | 6 | 11 | 19 | 62 | 7 | 13 | 19 | 57 | 8 | 16 | 25 | 74 |
| D10 | 3 | 3 | 4 | 6 | 7 | 9 | 15 | 55 | 3* | 11 | 17 | 60 | 3 | 11 | 19 | 76 |
| D11 | 4 | 5 | 5 | 6 | 6 | 10 | 16 | 63 | 6 | 12 | 18 | 53 | 8 | 17 | 25 | 78 |
| D14 | 3 | 4 | 4 | 8 | 4 | 10 | 15 | 60 | 7 | 12 | 19 | 57 | 9 | 16 | 24 | 81 |
| D16 | 3 | 4 | 4 | 5 | 5 | 10 | 16 | 61 | 7 | 14 | 21 | 57 | 7 | 17 | 26 | 86 |
| D17 | 3 | 4 | 5 | 5 | 5 | 11 | 16 | 63 | 7 | 13 | 19 | 55 | 8 | 15 | 21 | 65 |
| D21 | 2 | 3 | 3 | 5 | 3 | 7# | 11 | 55# | 8 | 16 | 22 | 59 | 8 | 16 | 22 | 72 |
| D22 | 3 | 3 | 5 | 7 | 5 | 13 | 20 | 66 | 7 | 10 | 14 | 50 | 8 | 15 | 22 | 70 |
| D25 | 3 | 4 | 4 | 6 | 5 | 11 | 17 | 65 | 6 | 12 | 17 | 54 | 9 | 17 | 23 | 66 |
| D28 | 2 | 3 | 3 | 5 | 5 | 10 | 17 | 61 | 6 | 14 | 19 | 56 | 6 | 15 | 21 | 77 |
| D29 | 2 | 4 | 5 | 6 | 4 | 11 | 17 | 60 | 8 | 12 | 18 | 57 | 9 | 16 | 24 | 76 |
| D31 | 4 | 6 | 7 | 9* | 6 | 14 | 21 | 63 | 5 | 10 | 15 | 53 | 6 | 13 | 18 | 69 |
| D32 | 4 | 4 | 5 | 6 | 7 | 15 | 19 | 65 | 4 | 9 | 15 | 49 | 4 | 9* | 17 | 69 |
| D35 | 4 | 4 | 4 | 8 | 5 | 11 | 17 | 64 | 6 | 12 | 17 | 53 | 8 | 17 | 24 | 79 |
| D38 | 3 | 3 | 4 | 7 | 4 | 9 | 15 | 64 | 6 | 13 | 18 | 56 | 6 | 13 | 20 | 74 |
| D49 | 2 | 3 | 6 | 6 | 5 | 12 | 17 | 64 | 8 | 12 | 18 | 55 | 8 | 17 | 25 | 75 |
| D50 | 3 | 7* | 7 | 7 | 7 | 12 | 19 | 60 | 4 | 12 | 17 | 56 | 5 | 15 | 21 | 74 |
| D51 | 4 | 5 | 5 | 6 | 6 | 11 | 18 | 56 | 6 | 12 | 17 | 58 | 6 | 14 | 23 | 75 |
| Mean | 3.05 | 4.27 | 4.86 | 6.36 | 5.27 | 10.91 | 17.18 | 61.82 | 6.18 | 12.14 | 17.50 | 55.00 | 6.95 | 14.73 | 21.82 | 72.86 |
| SD | 0.88 | 1.09 | 1.10 | 1.11 | 1.09 | 1.73 | 2.12 | 3.23 | 1.30 | 1.63 | 1.99 | 3.06 | 1.55 | 2.09 | 2.48 | 5.64 |
| Reference | 2.74 ± 0.84 | 3.79 ± 0.92 | 4.47 ± 0.94 | 6.22 ± 0.90 | 5.26 ± 1.03 | 11.41 ± 1.26 | 17.61 ± 1.40 | 62.16 ± 2.13 | 6.56 ± 1.18 | 12.28 ± 1.55 | 17.87 ± 1.75 | 55.78 ± 2.65 | 7.54 ± 1.40 | 15.02 ± 1.97 | 22.63 ± 2.48 | 75.13 ± 4.15 |
| P-value | 0.13 | 0.06 | 0.12 | 0.56 | 0.96 | 0.20 | 0.37 | 0.63 | 0.20 | 0.69 | 0.41 | 0.26 | 0.10 | 0.53 | 0.15 | 0.08 |
*The value was beyond (mean + 3*SD) of the reference sequence for LCS and LCSeq or (mean – 3*SD) of the reference sequence for Levenshtein distance and Hamming sequence, which was considered as unusual high similarity. #The value was beyond (mean – 3*SD) of the reference sequence for LCS and LCSeq or (mean + 3*SD) of the reference sequence for Levenshtein distance and Hamming sequence, which was considered as unusual low similarity. P < 0.05 was considered as a statistically significant difference in similarity between test sequences and references. LCS, longest common substring; LCSeq, longest common subsequence; SD, standard deviation.