miRNA: 3'- -AGgUAGUCCCUCAAaCA------------UCGAAGGUU- -5'
miRNA: 3'- aGGUa--GUCCCuCAAACAUCGaAGGUU- -5'
miRNA: 3'- -AGGU-AGUCCCUCA--------AACAU--CGAAGGuu -5'
miRNA: 3'- -AGGUAGUCCCUCAAACAUCGAAGGUU- -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 | |||||||
| 20997 | 3' | -50.4 | NC_004735.1 | + | 91559 | 0.68 | 0.964926 |
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Target: 5'- gUUgAUCAGGGAGUUcGUcuacaacuucauAGUUUCCGGa -3' miRNA: 3'- -AGgUAGUCCCUCAAaCA------------UCGAAGGUU- -5' |
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| 20997 | 3' | -50.4 | NC_004735.1 | + | 120339 | 0.68 | 0.953284 |
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Target: 5'- gUCAgcaCGGGGuGUUUGUGGUaUCCGAc -3' miRNA: 3'- aGGUa--GUCCCuCAAACAUCGaAGGUU- -5' |
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| 20997 | 3' | -50.4 | NC_004735.1 | + | 39251 | 0.73 | 0.766377 |
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Target: 5'- cUCCAcUCAGGGAGUcgccaaauUUGUGgcGCUUCCu- -3' miRNA: 3'- -AGGU-AGUCCCUCA--------AACAU--CGAAGGuu -5' |
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| 20997 | 3' | -50.4 | NC_004735.1 | + | 123105 | 1.07 | 0.008337 |
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Target: 5'- uUCCAUCAGGGAGUUUGUAGCUUCCAAg -3' miRNA: 3'- -AGGUAGUCCCUCAAACAUCGAAGGUU- -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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