miRNA: 3'- -GCGUUAGCuGGGAUUGCGcGUGGACu -5'
miRNA: 3'- -GCGUUAGC----UGGGa--UUGCgCGUGGACU- -5'
miRNA: 3'- gCGUuaGCUGGGauuGCGCG--UGGACU- -5'
Results 21 - 23 of 23 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 12428 | 3' | -53.8 | NC_003324.1 | + | 48378 | 0.71 | 0.499782 |
|
Target: 5'- uCGCAGUUGcCCUUGGCGCcUACCUGc -3' miRNA: 3'- -GCGUUAGCuGGGAUUGCGcGUGGACu -5' |
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| 12428 | 3' | -53.8 | NC_003324.1 | + | 49412 | 0.69 | 0.652056 |
|
Target: 5'- uCGCGAUCGgcgaGCCCggcAGCG-GCGCUUGGc -3' miRNA: 3'- -GCGUUAGC----UGGGa--UUGCgCGUGGACU- -5' |
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| 12428 | 3' | -53.8 | NC_003324.1 | + | 51161 | 0.68 | 0.685091 |
|
Target: 5'- gGCAggUGACCUgc-CGCGUcaACCUGAc -3' miRNA: 3'- gCGUuaGCUGGGauuGCGCG--UGGACU- -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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