miRNA: 3'- -UAGGGAGUUUUGCUCCCUUUUAGGGG- -5'
miRNA: 3'- -UAGGGAGUUUuGCUCCCUuu---UAGGGG- -5'
miRNA: 3'- -UAGGGaGUUuuGCUCCCUuu----UAGGGG- -5'
miRNA: 3'- uAGGGAGUuuUGcuCCCUuUUAGGGG- -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 | |||||||
| 2388 | 3' | -49.5 | NC_001416.1 | + | 38994 | 1.11 | 0.002493 |
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Target: 5'- cAUCCCUCAAAACGAGGGAAAAUCCCCu -3' miRNA: 3'- -UAGGGAGUUUUGCUCCCUUUUAGGGG- -5' |
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| 2388 | 3' | -49.5 | NC_001416.1 | + | 39038 | 0.81 | 0.233585 |
|
Target: 5'- cAUCCCUCAAAuUGGGGGAuugcuAUCCCUc -3' miRNA: 3'- -UAGGGAGUUUuGCUCCCUuu---UAGGGG- -5' |
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| 2388 | 3' | -49.5 | NC_001416.1 | + | 39106 | 0.72 | 0.655601 |
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Target: 5'- aAUCCCcCAAuuUGAGGGAuguuuuAUCCCUc -3' miRNA: 3'- -UAGGGaGUUuuGCUCCCUuu----UAGGGG- -5' |
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| 2388 | 3' | -49.5 | NC_001416.1 | + | 10837 | 0.67 | 0.896966 |
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Target: 5'- cUCCUUCG--GC--GGGAuGAUCCCCa -3' miRNA: 3'- uAGGGAGUuuUGcuCCCUuUUAGGGG- -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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