miRNA: 3'- -CCUAAUAAAGUGGGAGUCUCUCUCCG- -5'
miRNA: 3'- ccuaauaaAGUGGGag--UCUCU--CUCCG- -5'
miRNA: 3'- ccUAAUaAAGUGGGa-----GUCUCUcUCCG- -5'
miRNA: 3'- ccuaauaAAGUGGGAGu-CUCUCU-CCg -5'
miRNA: 3'- cCUAauaaAGugGG--AGUCUCUCUCCG- -5'
Results 1 - 5 of 5 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 | |||||||
| 2392 | 5' | -47.6 | NC_001416.1 | + | 46293 | 1.16 | 0.002117 |
|
Target: 5'- gGGAUUAUUUCACCCUCAGAGAGAGGCu -3' miRNA: 3'- -CCUAAUAAAGUGGGAGUCUCUCUCCG- -5' |
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| 2392 | 5' | -47.6 | NC_001416.1 | + | 33064 | 0.66 | 0.975627 |
|
Target: 5'- -------cUCGCCCgugaAGAGAaaGAGGCa -3' miRNA: 3'- ccuaauaaAGUGGGag--UCUCU--CUCCG- -5' |
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| 2392 | 5' | -47.6 | NC_001416.1 | + | 7292 | 0.67 | 0.965833 |
|
Target: 5'- -aGUUG-UUCACCCagcgagCGGAGAcGGGCa -3' miRNA: 3'- ccUAAUaAAGUGGGa-----GUCUCUcUCCG- -5' |
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| 2392 | 5' | -47.6 | NC_001416.1 | + | 5386 | 0.67 | 0.962027 |
|
Target: 5'- ------aUUCGCCCUCcuGAGAGAcGGg -3' miRNA: 3'- ccuaauaAAGUGGGAGu-CUCUCU-CCg -5' |
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| 2392 | 5' | -47.6 | NC_001416.1 | + | 46334 | 0.72 | 0.771846 |
|
Target: 5'- cGGUg---UCugCCagUCGGGGGGAGGCu -3' miRNA: 3'- cCUAauaaAGugGG--AGUCUCUCUCCG- -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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