miRNA: 3'- -AAGCUCGUGCUGu----------AGGGUUAGa---UCUU- -5'
miRNA: 3'- aaGCUCGUGcUGUAGGGUUAGau-CUu -5'
miRNA: 3'- aAGcUCGUGCUgu----AGGGUUAGAUCUu -5'
miRNA: 3'- -AAGCUCGUGCUGUAGGGUUAGAUCUU- -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 | |||||||
| 22528 | 3' | -51 | NC_005083.1 | + | 15670 | 0.67 | 0.993968 |
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Target: 5'- aUUCGAGCACGAUuuuacuaaaguUCCCGAUUaccaAGAGc -3' miRNA: 3'- -AAGCUCGUGCUGu----------AGGGUUAGa---UCUU- -5' |
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| 22528 | 3' | -51 | NC_005083.1 | + | 168996 | 0.67 | 0.991989 |
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Target: 5'- -aUGAGCGC-ACAUCCCAGUUguuGAc -3' miRNA: 3'- aaGCUCGUGcUGUAGGGUUAGau-CUu -5' |
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| 22528 | 3' | -51 | NC_005083.1 | + | 148424 | 0.72 | 0.905917 |
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Target: 5'- gUC-AGCGCGAagugcuUCCCAGUCUAGAu -3' miRNA: 3'- aAGcUCGUGCUgu----AGGGUUAGAUCUu -5' |
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| 22528 | 3' | -51 | NC_005083.1 | + | 78062 | 1.04 | 0.022224 |
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Target: 5'- cUUCGAGCACGACAUCCCAAUCUAGAAa -3' miRNA: 3'- -AAGCUCGUGCUGUAGGGUUAGAUCUU- -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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