miRNA: 3'- -CGGCGuCGGa---GACAGuacCUUCGGUG- -5'
miRNA: 3'- -CGGCGUCGGaGaCaGUaCCUUCG-GUG- -5'
miRNA: 3'- -CGGCGUCGGAGA----------CAGUaCCuuC-GGUG- -5'
miRNA: 3'- -CGGCGUCGGAGACAGUACCUUCGGUG- -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 | |||||||
| 6014 | 3' | -56.5 | NC_001809.1 | + | 57 | 0.66 | 0.183451 |
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Target: 5'- uGCCGCuGCCaaagCUGUCc--GAAGCUAUc -3' miRNA: 3'- -CGGCGuCGGa---GACAGuacCUUCGGUG- -5' |
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| 6014 | 3' | -56.5 | NC_001809.1 | + | 4065 | 0.68 | 0.134405 |
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Target: 5'- gGCUGCAGCCgCaGcCA-GGAAGCaCACa -3' miRNA: 3'- -CGGCGUCGGaGaCaGUaCCUUCG-GUG- -5' |
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| 6014 | 3' | -56.5 | NC_001809.1 | + | 211 | 0.7 | 0.10418 |
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Target: 5'- cGUCGCGGUCUCUuucgacacucGUCGaGGggGaCCGCc -3' miRNA: 3'- -CGGCGUCGGAGA----------CAGUaCCuuC-GGUG- -5' |
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| 6014 | 3' | -56.5 | NC_001809.1 | + | 7506 | 1.11 | 3.8e-05 |
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Target: 5'- aGCCGCAGCCUCUGUCAUGGAAGCCACu -3' miRNA: 3'- -CGGCGUCGGAGACAGUACCUUCGGUG- -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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