miRNA: 3'- -GGCUaUCGCUGAUUGAUGUCCcGGaa -5'
miRNA: 3'- gGCUA--UCGCUGAUUGa----UGUCCC------GGAA- -5'
miRNA: 3'- gGCUA---UCGCUGAUUGAuGUCCCGGAa -5'
miRNA: 3'- -GGCUAUCGCUGAUUGAUGUCCCGGAA- -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 | |||||||
| 33014 | 3' | -52 | NC_007456.1 | + | 1025 | 0.66 | 0.767547 |
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Target: 5'- aCUGAgAGUGAUUAACUACAGG-UCg- -3' miRNA: 3'- -GGCUaUCGCUGAUUGAUGUCCcGGaa -5' |
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| 33014 | 3' | -52 | NC_007456.1 | + | 33543 | 0.66 | 0.756761 |
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Target: 5'- uUGAUgaAGCGACUAAUgucagGCAGGGaugugaCCUUa -3' miRNA: 3'- gGCUA--UCGCUGAUUGa----UGUCCC------GGAA- -5' |
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| 33014 | 3' | -52 | NC_007456.1 | + | 4554 | 0.73 | 0.392638 |
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Target: 5'- gUGAUgccAGCGAUUGACU-CAGGGUCUg -3' miRNA: 3'- gGCUA---UCGCUGAUUGAuGUCCCGGAa -5' |
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| 33014 | 3' | -52 | NC_007456.1 | + | 703 | 1.07 | 0.001804 |
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Target: 5'- gCCGAUAGCGACUAACUACAGGGCCUUu -3' miRNA: 3'- -GGCUAUCGCUGAUUGAUGUCCCGGAA- -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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