miRNA: 3'- -AGGGAaGUUGg--UGGUgGCa---UUGACCC- -5'
miRNA: 3'- aGGgaagUUGGUGGU--GGCAUUGACCc -5'
miRNA: 3'- -AGGGAAGu---UGGUGGU---GGCAuu------GACCC- -5'
miRNA: 3'- aGGGAAGUUGGUGGuggcAUUGACCC- -5'
miRNA: 3'- -AGGGAAGUUGGUGGUGGCAUUGACCC- -5'
Results 1 - 5 of 5 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 | |||||||
| 4362 | 3' | -52.6 | NC_001720.1 | + | 38149 | 0.66 | 0.825928 |
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Target: 5'- cUUCCUgCAGCagaACCAgCGguucAGCUGGGu -3' miRNA: 3'- -AGGGAaGUUGg--UGGUgGCa---UUGACCC- -5' |
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| 4362 | 3' | -52.6 | NC_001720.1 | + | 36195 | 0.69 | 0.645336 |
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Target: 5'- gCCaagaGACCACCAccCCGUGAUUGGa -3' miRNA: 3'- aGGgaagUUGGUGGU--GGCAUUGACCc -5' |
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| 4362 | 3' | -52.6 | NC_001720.1 | + | 30414 | 0.7 | 0.58888 |
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Target: 5'- aUCCUUUCugacACCACCGauuCCGUuuacuuauCUGGGg -3' miRNA: 3'- -AGGGAAGu---UGGUGGU---GGCAuu------GACCC- -5' |
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| 4362 | 3' | -52.6 | NC_001720.1 | + | 16058 | 0.71 | 0.533363 |
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Target: 5'- gCUCUUCAACCACU----UGGCUGGGa -3' miRNA: 3'- aGGGAAGUUGGUGGuggcAUUGACCC- -5' |
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| 4362 | 3' | -52.6 | NC_001720.1 | + | 19777 | 1.13 | 0.000879 |
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Target: 5'- aUCCCUUCAACCACCACCGUAACUGGGg -3' miRNA: 3'- -AGGGAAGUUGGUGGUGGCAUUGACCC- -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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