miRNA: 3'- -GCgCAugCGa-------CCCGCCAUaCAACUau -5'
miRNA: 3'- gcGCAUGCGa-CCCGCCAU--ACAa-CUau -5'
miRNA: 3'- -GCGCAUGcGACCCGCCAUACa---ACUau -5'
miRNA: 3'- -GCGCAUGCGACCCGCCAUACAACUAU- -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 | |||||||
| 2918 | 5' | -53.1 | NC_001493.1 | + | 60093 | 0.66 | 0.963556 |
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Target: 5'- aCGgGUugGCgaggucgaGGGUGGUG-GUUGAa- -3' miRNA: 3'- -GCgCAugCGa-------CCCGCCAUaCAACUau -5' |
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| 2918 | 5' | -53.1 | NC_001493.1 | + | 43699 | 0.66 | 0.956136 |
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Target: 5'- -aUGUGCGCgaGGGCGGUGuuUGUggGAg- -3' miRNA: 3'- gcGCAUGCGa-CCCGCCAU--ACAa-CUau -5' |
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| 2918 | 5' | -53.1 | NC_001493.1 | + | 77777 | 0.67 | 0.927963 |
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Target: 5'- cCGUGUAC-UUGGGUGGUGUGaacgUGGc- -3' miRNA: 3'- -GCGCAUGcGACCCGCCAUACa---ACUau -5' |
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| 2918 | 5' | -53.1 | NC_001493.1 | + | 44337 | 1.07 | 0.005531 |
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Target: 5'- gCGCGUACGCUGGGCGGUAUGUUGAUAg -3' miRNA: 3'- -GCGCAUGCGACCCGCCAUACAACUAU- -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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