miRNA: 3'- -CCAGACGACCUAGCUCUACGGCAUCU- -5'
miRNA: 3'- ccaGACGACCuaGCUCUa-----------CGGCAUCU- -5'
miRNA: 3'- -CCAGa----------CGACCuaGCUCUA-CGGCAUCu -5'
miRNA: 3'- -CCAGa-CG-ACCUAGCUCU------ACGGcaucu -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 | |||||||
| 348 | 5' | -52.9 | AC_000011.1 | + | 5134 | 1.12 | 0.000662 |
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Target: 5'- aGGUCUGCUGGAUCGAGAUGCCGUAGAg -3' miRNA: 3'- -CCAGACGACCUAGCUCUACGGCAUCU- -5' |
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| 348 | 5' | -52.9 | AC_000011.1 | + | 10941 | 0.69 | 0.569328 |
|
Target: 5'- --gCUGCUGGggCGGGGgcagaagcgccgGCUGUGGAg -3' miRNA: 3'- ccaGACGACCuaGCUCUa-----------CGGCAUCU- -5' |
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| 348 | 5' | -52.9 | AC_000011.1 | + | 16578 | 0.69 | 0.571596 |
|
Target: 5'- aGGUCacgggcuugagGCUGGcgUGGGGUuGCCGUGGu -3' miRNA: 3'- -CCAGa----------CGACCuaGCUCUA-CGGCAUCu -5' |
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| 348 | 5' | -52.9 | AC_000011.1 | + | 10575 | 0.66 | 0.730938 |
|
Target: 5'- uGGUCagGCuUGGGUCGAGAcgggagUGCCa---- -3' miRNA: 3'- -CCAGa-CG-ACCUAGCUCU------ACGGcaucu -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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