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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
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Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 2387 | 3' | -37 | NC_001416.1 | + | 37822 | 0.71 | 0.999994 |
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Target: 5'- ----gGGGCAgucag-GCGUUGGUGCu -3' miRNA: 3'- caauaUUCGUaaauuaCGUAACUACG- -5' |
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| 2387 | 3' | -37 | NC_001416.1 | + | 37717 | 1.17 | 0.032829 |
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Target: 5'- cGUUAUAAGCAUUUAAUGCAUUGAUGCc -3' miRNA: 3'- -CAAUAUUCGUAAAUUACGUAACUACG- -5' |
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| 2387 | 3' | -37 | NC_001416.1 | + | 30205 | 0.7 | 0.999999 |
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Target: 5'- -----cGGCGUUUGAUGUAUUGcUGg -3' miRNA: 3'- caauauUCGUAAAUUACGUAACuACg -5' |
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| 2387 | 3' | -37 | NC_001416.1 | + | 34690 | 0.66 | 1 |
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Target: 5'- -aUAUAAGCgAUUUAAgcuaagaaaacGCAUUaaGAUGCa -3' miRNA: 3'- caAUAUUCG-UAAAUUa----------CGUAA--CUACG- -5' |
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| 2387 | 3' | -37 | NC_001416.1 | + | 47829 | 0.66 | 1 |
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Target: 5'- ----aGAGCAaUUGAggcaGCGUUGGUGa -3' miRNA: 3'- caauaUUCGUaAAUUa---CGUAACUACg -5' |
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| 2387 | 3' | -37 | NC_001416.1 | + | 43406 | 0.66 | 1 |
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Target: 5'- --cAUGAGCAaaUGAUG-AUUGAUGg -3' miRNA: 3'- caaUAUUCGUaaAUUACgUAACUACg -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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