miRNA: 3'- gC-GGGGGGugGAAAAAC-CCuguUUGa -5'
miRNA: 3'- gC-GGGGGGugGAAA--------AACCCU---GUUUGA- -5'
miRNA: 3'- gCGGGGGGUGGAAAAACccu-GUUUGa -5'
miRNA: 3'- -GCGGGGGGUGGAAAAACCCUGUUUGA- -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 | |||||||
| 11217 | 5' | -53.1 | NC_003038.1 | + | 185226 | 0.66 | 0.986391 |
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Target: 5'- aGaCCCCCCugCUUUUUGcGGu--AACc -3' miRNA: 3'- gC-GGGGGGugGAAAAAC-CCuguUUGa -5' |
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| 11217 | 5' | -53.1 | NC_003038.1 | + | 185017 | 0.67 | 0.970861 |
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Target: 5'- uGaCCCCCCugCUUUuuaauuggUUGGGAuuuCAAAUUc -3' miRNA: 3'- gC-GGGGGGugGAAA--------AACCCU---GUUUGA- -5' |
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| 11217 | 5' | -53.1 | NC_003038.1 | + | 134390 | 0.78 | 0.524241 |
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Target: 5'- uGCCCCCCACCUUUUUGauuuCAGAUa -3' miRNA: 3'- gCGGGGGGUGGAAAAACccu-GUUUGa -5' |
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| 11217 | 5' | -53.1 | NC_003038.1 | + | 134599 | 1.08 | 0.009061 |
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Target: 5'- gCGCCCCCCACCUUUUUGGGACAAACUu -3' miRNA: 3'- -GCGGGGGGUGGAAAAACCCUGUUUGA- -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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