miRNA: 3'- gGUACCUCUgcaAGUUGUauaaGGGa -5'
miRNA: 3'- gGUACCUcUGCAAGUUGUAUAa---------GGGa -5'
miRNA: 3'- -GGUa---CCUCU-GCAAGUUGUauaaGGGa -5'
miRNA: 3'- -GGUACCucug-CAa--GUUGU--AUAAGGGA- -5'
miRNA: 3'- -GGUACCUCUGCAAGUUGUAUAAGGGA- -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
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| Predicted miRNA align pattern | |||||||
| 8740 | 5' | -46.8 | NC_002331.1 | + | 76307 | 0.66 | 0.999952 |
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Target: 5'- aCAUGGAGAa--UCGGCAguugCCCa -3' miRNA: 3'- gGUACCUCUgcaAGUUGUauaaGGGa -5' |
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| 8740 | 5' | -46.8 | NC_002331.1 | + | 59237 | 0.67 | 0.999936 |
|
Target: 5'- aCGUGGAcAUGUUCAACGUGUggcgugaaugCCUc -3' miRNA: 3'- gGUACCUcUGCAAGUUGUAUAa---------GGGa -5' |
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| 8740 | 5' | -46.8 | NC_002331.1 | + | 62286 | 0.67 | 0.999916 |
|
Target: 5'- uCCAaacgGGAGAuUGUUCAACAcg--CCCa -3' miRNA: 3'- -GGUa---CCUCU-GCAAGUUGUauaaGGGa -5' |
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| 8740 | 5' | -46.8 | NC_002331.1 | + | 86759 | 0.68 | 0.999699 |
|
Target: 5'- cCCAUGGucaaaGUgcgCGACAggUGUUCCCUg -3' miRNA: 3'- -GGUACCucug-CAa--GUUGU--AUAAGGGA- -5' |
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| 8740 | 5' | -46.8 | NC_002331.1 | + | 156864 | 1.11 | 0.022689 |
|
Target: 5'- cCCAUGGAGACGUUCAACAUAUUCCCUc -3' miRNA: 3'- -GGUACCUCUGCAAGUUGUAUAAGGGA- -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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