miRNA: 3'- cGGGuuuUAG-CACCUAUUa------GGCCUGG- -5'
miRNA: 3'- -CGGguuUUAGCACCuauuAGGCCUGG- -5'
miRNA: 3'- -CGGGUUU---UAGcACCUa------UUAGGCCUGG- -5'
miRNA: 3'- -CGGGUUUUAGCACCUAUUAGGCCUGG- -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 | |||||||
| 830 | 5' | -47.9 | NC_000874.1 | + | 2774 | 0.68 | 0.386376 |
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Target: 5'- uCCCu--GUCuGUGGAUAAgccnaaaCCGGGCUu -3' miRNA: 3'- cGGGuuuUAG-CACCUAUUa------GGCCUGG- -5' |
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| 830 | 5' | -47.9 | NC_000874.1 | + | 3712 | 0.71 | 0.25251 |
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Target: 5'- gGCCaguGGUCGUGG----UCCGGGCUc -3' miRNA: 3'- -CGGguuUUAGCACCuauuAGGCCUGG- -5' |
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| 830 | 5' | -47.9 | NC_000874.1 | + | 3027 | 0.72 | 0.221995 |
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Target: 5'- cGCCCAAAcucAUCcUGGAgugcaaaAAUCUGGAUCu -3' miRNA: 3'- -CGGGUUU---UAGcACCUa------UUAGGCCUGG- -5' |
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| 830 | 5' | -47.9 | NC_000874.1 | + | 5102 | 1.15 | 0.000107 |
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Target: 5'- cGCCCAAAAUCGUGGAUAAUCCGGACCc -3' miRNA: 3'- -CGGGUUUUAGCACCUAUUAGGCCUGG- -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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