miRNA: 3'- guaAGGCAGAGG------UGGCGACCCauuuu -5'
miRNA: 3'- guaagGCAGAGGUGG------CGACCCAuuuu -5'
miRNA: 3'- guaAggCAGAGGUGG--------------CGACCCAUuuu -5'
miRNA: 3'- -GUAAGGCAGAGGUGGCGACCCAUUUU- -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 | |||||||
| 29357 | 3' | -52.5 | NC_006150.1 | + | 219153 | 0.66 | 0.989808 |
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Target: 5'- --cUUCGUCUUCcucgggACCGCUGGGa---- -3' miRNA: 3'- guaAGGCAGAGG------UGGCGACCCauuuu -5' |
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| 29357 | 3' | -52.5 | NC_006150.1 | + | 8751 | 0.68 | 0.962075 |
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Target: 5'- ----aCGUCUCCGCCgaagguGCUGGGUu--- -3' miRNA: 3'- guaagGCAGAGGUGG------CGACCCAuuuu -5' |
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| 29357 | 3' | -52.5 | NC_006150.1 | + | 194422 | 0.69 | 0.953445 |
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Target: 5'- --aUuuGUCUCCACUggaucagaccucuaGCUGGGUGu-- -3' miRNA: 3'- guaAggCAGAGGUGG--------------CGACCCAUuuu -5' |
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| 29357 | 3' | -52.5 | NC_006150.1 | + | 215338 | 1.06 | 0.012045 |
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Target: 5'- aCAUUCCGUCUCCACCGCUGGGUAAAAc -3' miRNA: 3'- -GUAAGGCAGAGGUGGCGACCCAUUUU- -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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