miRNA: 3'- cuuCUGAU-GUCGCGCU-----AGGa----CAGGCG- -5'
miRNA: 3'- -CUUCUGAUG--------------UCGCGCUAGgACAGgCG- -5'
miRNA: 3'- cuUCUGAUGUC-GCGCUAGGaCAGGCG- -5'
miRNA: 3'- -CUUCUGAUGUCGCGCUAGGACAGGCG- -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 | |||||||
| 18016 | 3' | -53.3 | NC_004665.1 | + | 32150 | 0.67 | 0.656637 |
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Target: 5'- --cGGCUGcCAGUGCGAgucaaUCCgcccaGUCUGCu -3' miRNA: 3'- cuuCUGAU-GUCGCGCU-----AGGa----CAGGCG- -5' |
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| 18016 | 3' | -53.3 | NC_004665.1 | + | 17214 | 0.69 | 0.539323 |
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Target: 5'- aGAAGGCUGCucgugccaagggcaAGCGUGGUC-UGUCgGUa -3' miRNA: 3'- -CUUCUGAUG--------------UCGCGCUAGgACAGgCG- -5' |
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| 18016 | 3' | -53.3 | NC_004665.1 | + | 19448 | 0.74 | 0.285952 |
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Target: 5'- -uGGGCUACAGuCGCGGUUUcGUUCGCu -3' miRNA: 3'- cuUCUGAUGUC-GCGCUAGGaCAGGCG- -5' |
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| 18016 | 3' | -53.3 | NC_004665.1 | + | 20600 | 1.12 | 0.000596 |
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Target: 5'- aGAAGACUACAGCGCGAUCCUGUCCGCu -3' miRNA: 3'- -CUUCUGAUGUCGCGCUAGGACAGGCG- -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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