miRNA: 3'- aGACCuCGaUUGGCGGCGa-------CGGUUUu -5'
miRNA: 3'- agaCCUcGAuUGGCGGCGaCGGUUuu -5'
miRNA: 3'- -AGACcuCGAUUGGCGGCg---ACGGuuuu -5'
miRNA: 3'- -AGACCUCGAUUGGCGGCGACGGUUUU- -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 | |||||||
| 16985 | 3' | -55.2 | NC_004323.1 | + | 3895 | 0.66 | 0.884807 |
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Target: 5'- aUUGG-GC-AGCCGCCGCccuucuuaGCCAGAc -3' miRNA: 3'- aGACCuCGaUUGGCGGCGa-------CGGUUUu -5' |
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| 16985 | 3' | -55.2 | NC_004323.1 | + | 85956 | 0.66 | 0.869956 |
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Target: 5'- --cGGAcCUcGCCGCCGC-GCCAAc- -3' miRNA: 3'- agaCCUcGAuUGGCGGCGaCGGUUuu -5' |
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| 16985 | 3' | -55.2 | NC_004323.1 | + | 123573 | 0.67 | 0.820108 |
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Target: 5'- cUCUGuuGCUGACCGUCGaacaUGCCu--- -3' miRNA: 3'- -AGACcuCGAUUGGCGGCg---ACGGuuuu -5' |
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| 16985 | 3' | -55.2 | NC_004323.1 | + | 107754 | 1.07 | 0.003162 |
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Target: 5'- aUCUGGAGCUAACCGCCGCUGCCAAAAu -3' miRNA: 3'- -AGACCUCGAUUGGCGGCGACGGUUUU- -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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