miRNA: 3'- -CGugCuCGGUCGA---UGA---------------GGUUGGaACG- -5'
miRNA: 3'- -CGUGCUCGGUCGa------UGAGGuUgGAACG- -5'
miRNA: 3'- cgUGCUC----------GGUCGAUGAGGUUGGa---ACG- -5'
miRNA: 3'- -CGUGCUCGGUCGAUGAGGUUGGAACG- -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 | |||||||
| 15297 | 5' | -52.9 | NC_003849.1 | + | 5752 | 0.66 | 0.214305 |
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Target: 5'- cGCugG-GCCGGCUuugACUucuucgacggccugcUCAACCcUGCg -3' miRNA: 3'- -CGugCuCGGUCGA---UGA---------------GGUUGGaACG- -5' |
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| 15297 | 5' | -52.9 | NC_003849.1 | + | 2528 | 0.69 | 0.129026 |
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Target: 5'- gGCACGAGUUGGCcgaguagACUCCcAgCUUGUu -3' miRNA: 3'- -CGUGCUCGGUCGa------UGAGGuUgGAACG- -5' |
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| 15297 | 5' | -52.9 | NC_003849.1 | + | 5063 | 0.7 | 0.101682 |
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Target: 5'- -gACGGGaccaaauccaUCAGCUACUUCAGCCccagUGCg -3' miRNA: 3'- cgUGCUC----------GGUCGAUGAGGUUGGa---ACG- -5' |
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| 15297 | 5' | -52.9 | NC_003849.1 | + | 5886 | 1.13 | 2.7e-05 |
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Target: 5'- aGCACGAGCCAGCUACUCCAACCUUGCc -3' miRNA: 3'- -CGUGCUCGGUCGAUGAGGUUGGAACG- -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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