miRNA: 3'- -UAGGCCACCGCGUCGUCGCACUUAGG- -5'
miRNA: 3'- -UAGGCCACCGC-GUCGUCGc----ACU-----UAGG- -5'
miRNA: 3'- uaGGCCACCG-----CG--------------UCGUCGCAcUUAGG- -5'
Results 1 - 3 of 3 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 | |||||||
| 21939 | 5' | -57.2 | NC_004913.1 | + | 20398 | 1.1 | 0.000504 |
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Target: 5'- gAUCCGGUGGCGCAGCAGCGUGAAUCCa -3' miRNA: 3'- -UAGGCCACCGCGUCGUCGCACUUAGG- -5' |
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| 21939 | 5' | -57.2 | NC_004913.1 | + | 24405 | 0.73 | 0.23095 |
|
Target: 5'- gAUCCGGUGGUGuCAGCGGUacacaUGAaggcuGUCCg -3' miRNA: 3'- -UAGGCCACCGC-GUCGUCGc----ACU-----UAGG- -5' |
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| 21939 | 5' | -57.2 | NC_004913.1 | + | 57755 | 0.66 | 0.616839 |
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Target: 5'- -gCCGGUGGCuucacGCacgguaccggagcaGGUGGCGUuGAUCCg -3' miRNA: 3'- uaGGCCACCG-----CG--------------UCGUCGCAcUUAGG- -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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