miRNA: 3'- -GCUaagUGACGUGCUGaaAGA---------AUGAU- -5'
miRNA: 3'- -GCUAaGUGACGUGC-UGAAAgAa---UGau -5'
miRNA: 3'- -GCuaAGUGa-CGUGCUGAa--AGAAugau -5'
miRNA: 3'- -GCUAAGUGACGUGCUGAAAGAAUGAU- -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 | |||||||
| 6516 | 3' | -45.4 | NC_001847.1 | + | 71719 | 0.66 | 0.999953 |
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Target: 5'- cCGAgg-ACUGCACGGCggUCUacaaggaccUGCUGg -3' miRNA: 3'- -GCUaagUGACGUGCUGaaAGA---------AUGAU- -5' |
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| 6516 | 3' | -45.4 | NC_001847.1 | + | 116031 | 0.66 | 0.999953 |
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Target: 5'- cCGGUgCACUGCGCGcACUUUgUgacgGCa- -3' miRNA: 3'- -GCUAaGUGACGUGC-UGAAAgAa---UGau -5' |
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| 6516 | 3' | -45.4 | NC_001847.1 | + | 80583 | 0.66 | 0.999937 |
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Target: 5'- gCGcgUCACggGCGCGACUgcgUCUUc--- -3' miRNA: 3'- -GCuaAGUGa-CGUGCUGAa--AGAAugau -5' |
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| 6516 | 3' | -45.4 | NC_001847.1 | + | 784 | 1.08 | 0.029081 |
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Target: 5'- cCGAUUCACUGCACGACUUUCUUACUAc -3' miRNA: 3'- -GCUAAGUGACGUGCUGAAAGAAUGAU- -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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