miRNA: 3'- -UCGUCUCCUGGAAAAAAACAAUGGAC- -5'
miRNA: 3'- -UCGUCUcCUGGaaAAAAACAAUGGac -5'
miRNA: 3'- -UCGUCUCCUGGAaAAAAACAAUggac -5'
miRNA: 3'- uCGUCUCCUGGAaaaaa-----ACA-----AUGGac -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 | |||||||
| 28227 | 5' | -45.4 | NC_005893.1 | + | 21768 | 1.11 | 0.00488 |
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Target: 5'- gAGCAGAGGACCUUUUUUUGUUACCUGa -3' miRNA: 3'- -UCGUCUCCUGGAAAAAAACAAUGGAC- -5' |
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| 28227 | 5' | -45.4 | NC_005893.1 | + | 22468 | 0.7 | 0.895729 |
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Target: 5'- gGGCAGAaGGCU--UUUUUGUUACCa- -3' miRNA: 3'- -UCGUCUcCUGGaaAAAAACAAUGGac -5' |
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| 28227 | 5' | -45.4 | NC_005893.1 | + | 21739 | 0.66 | 0.983762 |
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Target: 5'- gGGUGGAGGGCUUaUUUUUGUUGg--- -3' miRNA: 3'- -UCGUCUCCUGGAaAAAAACAAUggac -5' |
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| 28227 | 5' | -45.4 | NC_005893.1 | + | 685 | 0.66 | 0.986665 |
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Target: 5'- cGCAGGGGACCUcacacaccagUGUccauuUGCCg- -3' miRNA: 3'- uCGUCUCCUGGAaaaaa-----ACA-----AUGGac -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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