miRNA: 3'- -UGGC-UCuuggCUUCGGGCUUGGu--UGG- -5'
miRNA: 3'- -UGGCUCUUGG--------CUUCGg----GCUUG-GUUGG- -5'
miRNA: 3'- -UGGCUCUUGGc----UUCGGGCU--UGGUUGG- -5'
miRNA: 3'- -UGGCUCUUGGCUUCGGGCUUGGUUGG- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 15620 | 3' | -53.7 | NC_004051.1 | + | 1434 | 0.66 | 0.081694 |
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Target: 5'- gACCGuAGuaa-GGAGUCCGGACCcacGCCg -3' miRNA: 3'- -UGGC-UCuuggCUUCGGGCUUGGu--UGG- -5' |
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| 15620 | 3' | -53.7 | NC_004051.1 | + | 380 | 0.66 | 0.078745 |
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Target: 5'- gGCUGAGAACUccuucgcaGAAGCgauggCGAACuCGACCc -3' miRNA: 3'- -UGGCUCUUGG--------CUUCGg----GCUUG-GUUGG- -5' |
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| 15620 | 3' | -53.7 | NC_004051.1 | + | 1212 | 0.79 | 0.005586 |
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Target: 5'- uGCUGAGGGCCaguacAGGCCCGAagACCAGCUa -3' miRNA: 3'- -UGGCUCUUGGc----UUCGGGCU--UGGUUGG- -5' |
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| 15620 | 3' | -53.7 | NC_004051.1 | + | 1690 | 1.11 | 0.000008 |
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Target: 5'- gACCGAGAACCGAAGCCCGAACCAACCc -3' miRNA: 3'- -UGGCUCUUGGCUUCGGGCUUGGUUGG- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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