miRNA: 3'- gAUAGUGACAGGGG-----CGU----UAUC-GCCCG- -5'
miRNA: 3'- gauAGUga-CAGGG-GCGU----UAUCGCCCG- -5'
miRNA: 3'- gauaGugACAGGGGCGUUaUCGCCcg -5'
miRNA: 3'- -GAUAGUGACAGGGGCGUUAUCGCCCG- -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 | |||||||
| 6039 | 3' | -53.8 | NC_001813.1 | + | 14034 | 0.69 | 0.459741 |
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Target: 5'- aUGUCACUGUUUCCaauacGCAggccAUAGaCGGGUg -3' miRNA: 3'- gAUAGUGACAGGGG-----CGU----UAUC-GCCCG- -5' |
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| 6039 | 3' | -53.8 | NC_001813.1 | + | 29858 | 0.69 | 0.449355 |
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Target: 5'- --uUCAgggGUCCCgCGCGucugAUAGUGGGCu -3' miRNA: 3'- gauAGUga-CAGGG-GCGU----UAUCGCCCG- -5' |
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| 6039 | 3' | -53.8 | NC_001813.1 | + | 5357 | 0.71 | 0.37128 |
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Target: 5'- ---cCugUGUUCCCGCAAaAGCGGa- -3' miRNA: 3'- gauaGugACAGGGGCGUUaUCGCCcg -5' |
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| 6039 | 3' | -53.8 | NC_001813.1 | + | 13886 | 1.13 | 0.000383 |
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Target: 5'- gCUAUCACUGUCCCCGCAAUAGCGGGCg -3' miRNA: 3'- -GAUAGUGACAGGGGCGUUAUCGCCCG- -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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