miRNA: 3'- -UUUAGGaa-GUGGa---CAGUAGUAUGGGU- -5'
miRNA: 3'- uuuAGGAAGUGGACAGUAguaUGGGu -5'
miRNA: 3'- uuUAgGAAGugGACAGU-----------AGUAUGGGU- -5'
miRNA: 3'- uuUAGGAaGUGGACAGU--AGUAUGGgu -5'
miRNA: 3'- -UUUAGGAAGUGGACAGUAGUAUGGGU- -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 | |||||||
| 32842 | 5' | -48.7 | NC_007346.1 | + | 304801 | 0.66 | 0.999981 |
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Target: 5'- aGAAUCCacgUACCagucGUCGUCAUAUCUAa -3' miRNA: 3'- -UUUAGGaa-GUGGa---CAGUAGUAUGGGU- -5' |
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| 32842 | 5' | -48.7 | NC_007346.1 | + | 72437 | 0.68 | 0.999785 |
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Target: 5'- --uUUCUUCAUCUGUCAUa--ACCCu -3' miRNA: 3'- uuuAGGAAGUGGACAGUAguaUGGGu -5' |
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| 32842 | 5' | -48.7 | NC_007346.1 | + | 61396 | 0.7 | 0.998593 |
|
Target: 5'- -cAUgUUUCugCUGUCAuuaacugaauuUCAUGCCCAu -3' miRNA: 3'- uuUAgGAAGugGACAGU-----------AGUAUGGGU- -5' |
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| 32842 | 5' | -48.7 | NC_007346.1 | + | 208440 | 0.71 | 0.997614 |
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Target: 5'- -cAUCCUcUGCCUGUCGcuUCAUGCCa- -3' miRNA: 3'- uuUAGGAaGUGGACAGU--AGUAUGGgu -5' |
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| 32842 | 5' | -48.7 | NC_007346.1 | + | 393030 | 1.08 | 0.03863 |
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Target: 5'- gAAAUCCUUCACCUGUCAUCAUACCCAg -3' miRNA: 3'- -UUUAGGAAGUGGACAGUAGUAUGGGU- -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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