miRNA: 3'- gGGuuUGGAgCAG-----------AGGA-GACGGGGGa -5'
miRNA: 3'- -GGGuuUGGAG------------CAG---------------AGGAGACGGGGGa -5'
miRNA: 3'- -GGGUuu-----GGAGCAGAGGa---------GACGGGGGa -5'
miRNA: 3'- -GGGUUUGGAGCAGAGGAGACGGGGGA- -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 | |||||||
| 7479 | 5' | -57.8 | NC_001918.1 | + | 2674 | 0.66 | 0.130991 |
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Target: 5'- gCC--GCCUgGUCgugugcuacacUCCUgCUGCCCCCc -3' miRNA: 3'- gGGuuUGGAgCAG-----------AGGA-GACGGGGGa -5' |
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| 7479 | 5' | -57.8 | NC_001918.1 | + | 6501 | 0.68 | 0.102865 |
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Target: 5'- uUCUggGCCUCcacgucgcuggaGUCgcgggcacgagcggaUUCUCUGCCCCCa -3' miRNA: 3'- -GGGuuUGGAG------------CAG---------------AGGAGACGGGGGa -5' |
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| 7479 | 5' | -57.8 | NC_001918.1 | + | 6313 | 0.7 | 0.071133 |
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Target: 5'- cCCCAcuggacuCCUUGUUUCCcaauucaaagCUGCCCCCc -3' miRNA: 3'- -GGGUuu-----GGAGCAGAGGa---------GACGGGGGa -5' |
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| 7479 | 5' | -57.8 | NC_001918.1 | + | 5248 | 1.08 | 3.9e-05 |
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Target: 5'- uCCCAAACCUCGUCUCCUCUGCCCCCUu -3' miRNA: 3'- -GGGUUUGGAGCAGAGGAGACGGGGGA- -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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