miRNA: 3'- -CGUGUUa----UGGGAGUGa--UUGGUGAagu -5'
miRNA: 3'- cgUGUUA-UGGGAGUGA--UUGGUGAAGu -5'
miRNA: 3'- -CGUGUuaUGGGAGUGAU--UGGUGAagu -5'
miRNA: 3'- -CGUGUUAUGGGAGUGAUUGGUGAAGU- -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 | |||||||
| 31576 | 5' | -47 | NC_006852.1 | + | 25687 | 0.67 | 0.916646 |
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Target: 5'- gGCACAAgaacaGCCCUUAUgugGAUCGCUa-- -3' miRNA: 3'- -CGUGUUa----UGGGAGUGa--UUGGUGAagu -5' |
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| 31576 | 5' | -47 | NC_006852.1 | + | 6928 | 0.67 | 0.909599 |
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Target: 5'- -gGCAAUaGCUUUCGCUuuGACCACUUUu -3' miRNA: 3'- cgUGUUA-UGGGAGUGA--UUGGUGAAGu -5' |
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| 31576 | 5' | -47 | NC_006852.1 | + | 20705 | 0.72 | 0.709755 |
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Target: 5'- uGCACAc-ACUCUCACUAcuACCACUg-- -3' miRNA: 3'- -CGUGUuaUGGGAGUGAU--UGGUGAagu -5' |
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| 31576 | 5' | -47 | NC_006852.1 | + | 9385 | 1.13 | 0.001903 |
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Target: 5'- cGCACAAUACCCUCACUAACCACUUCAg -3' miRNA: 3'- -CGUGUUAUGGGAGUGAUUGGUGAAGU- -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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