miRNA: 3'- gguuCGCAA--ACCGAGACU-CAAC----UAUC- -5'
miRNA: 3'- -GGU-UCGcAAACCG------AGACUCA-ACUAUC- -5'
miRNA: 3'- -GGU--UCGCAAACCGAga-CUCAACUa--UC- -5'
miRNA: 3'- -GGUUCGCAAACCGAGACUCAACUAUC- -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 | |||||||
| 23547 | 3' | -47.3 | NC_005260.1 | + | 102682 | 0.67 | 0.999911 |
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Target: 5'- ---uGCGUUugUGGCUCUGAuGUUGuuuaAUAGc -3' miRNA: 3'- gguuCGCAA--ACCGAGACU-CAAC----UAUC- -5' |
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| 23547 | 3' | -47.3 | NC_005260.1 | + | 49676 | 0.71 | 0.996706 |
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Target: 5'- aCCAgAGCuUUUGGCuuaauaUCUGAGUgUGGUAGg -3' miRNA: 3'- -GGU-UCGcAAACCG------AGACUCA-ACUAUC- -5' |
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| 23547 | 3' | -47.3 | NC_005260.1 | + | 187769 | 0.79 | 0.835698 |
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Target: 5'- gCCAggAGCGUUUGGCUaaaGAGUUGAgggAGa -3' miRNA: 3'- -GGU--UCGCAAACCGAga-CUCAACUa--UC- -5' |
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| 23547 | 3' | -47.3 | NC_005260.1 | + | 187467 | 1.11 | 0.022415 |
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Target: 5'- gCCAAGCGUUUGGCUCUGAGUUGAUAGc -3' miRNA: 3'- -GGUUCGCAAACCGAGACUCAACUAUC- -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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