miRNA: 3'- -GGGGga--CUugGGUCCuau--UGGGAGUU- -5'
miRNA: 3'- -GGGGGa--------CUUGGGUCCUauUGGGAGuu -5'
miRNA: 3'- -GGGGGACUUGGGUCCuaUUGGG--AGUu -5'
miRNA: 3'- -GGGGGACUUGGGUCCUAUUGGGAGUU- -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 | |||||||
| 6072 | 5' | -55.3 | NC_001819.1 | + | 4980 | 0.67 | 0.151995 |
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Target: 5'- uUCCCagugGGugCCGGGucgguGCCCUCGAa -3' miRNA: 3'- -GGGGga--CUugGGUCCuau--UGGGAGUU- -5' |
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| 6072 | 5' | -55.3 | NC_001819.1 | + | 1100 | 0.73 | 0.054525 |
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Target: 5'- cCCUCCgccuuaccgGGACCCAGGGccACCCUCu- -3' miRNA: 3'- -GGGGGa--------CUUGGGUCCUauUGGGAGuu -5' |
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| 6072 | 5' | -55.3 | NC_001819.1 | + | 2395 | 0.75 | 0.038819 |
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Target: 5'- gCCCCUUGGACCCAGGc-AGCCUugUCAc -3' miRNA: 3'- -GGGGGACUUGGGUCCuaUUGGG--AGUu -5' |
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| 6072 | 5' | -55.3 | NC_001819.1 | + | 2254 | 1.08 | 6.3e-05 |
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Target: 5'- cCCCCCUGAACCCAGGAUAACCCUCAAa -3' miRNA: 3'- -GGGGGACUUGGGUCCUAUUGGGAGUU- -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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