miRNA: 3'- -CCGCUGGGCGC-------------GGUUAUuCGGUuacu -5'
miRNA: 3'- cCGCUGGGcGCGGUUAU---UCGgUUACU- -5'
miRNA: 3'- -CCGCUGGGCGCGGUUAUUCgGUUACU- -5'
Results 1 - 3 of 3 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
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Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 1179 | 3' | -53.3 | NC_001132.2 | + | 37889 | 0.68 | 0.916697 |
|
Target: 5'- uGGCGGCCUGCGuauucgauuuaguCCGAUAcGCCGu--- -3' miRNA: 3'- -CCGCUGGGCGC-------------GGUUAUuCGGUuacu -5' |
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| 1179 | 3' | -53.3 | NC_001132.2 | + | 128821 | 0.71 | 0.79533 |
|
Target: 5'- uGCGACCC-CGCCAGUAuguAGUaGAUGGa -3' miRNA: 3'- cCGCUGGGcGCGGUUAU---UCGgUUACU- -5' |
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| 1179 | 3' | -53.3 | NC_001132.2 | + | 158800 | 0.98 | 0.026836 |
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Target: 5'- cGGCGACCCGCGCCAAUAAG-CAAUGAu -3' miRNA: 3'- -CCGCUGGGCGCGGUUAUUCgGUUACU- -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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