miRNA: 3'- -AGAgUACCGUcGGGGAGc-GGCGGAug -5'
miRNA: 3'- aGAGua-CCGUCGGGGa-----------GCGGCGGaug -5'
miRNA: 3'- aGAGU----ACCGUCGGGGaGCGGcGGAUG- -5'
miRNA: 3'- -AGAGUACCGUCGGGGAGCGGCGGAUG- -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 | |||||||
| 735 | 5' | -60.4 | AC_000020.1 | + | 27268 | 0.66 | 0.270112 |
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Target: 5'- cUUUgGUGGCAaCCCCUCccCCGCCUc- -3' miRNA: 3'- -AGAgUACCGUcGGGGAGc-GGCGGAug -5' |
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| 735 | 5' | -60.4 | AC_000020.1 | + | 14365 | 0.68 | 0.206016 |
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Target: 5'- aCUCuccGGCAGCCUCcagcaccaagcgCGCCGCCg-- -3' miRNA: 3'- aGAGua-CCGUCGGGGa-----------GCGGCGGaug -5' |
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| 735 | 5' | -60.4 | AC_000020.1 | + | 14731 | 0.7 | 0.136619 |
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Target: 5'- gCUCAuccuUGGCAGCCCUgCGCUuUCUGCu -3' miRNA: 3'- aGAGU----ACCGUCGGGGaGCGGcGGAUG- -5' |
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| 735 | 5' | -60.4 | AC_000020.1 | + | 595 | 1.09 | 0.000121 |
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Target: 5'- uUCUCAUGGCAGCCCCUCGCCGCCUACu -3' miRNA: 3'- -AGAGUACCGUCGGGGAGCGGCGGAUG- -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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