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miRNA: 3'- -CAUGUCGUGACACCGACCGGUAGACG- -5'
miRNA: 3'- caUGUCG-------------UGACACCGa-CCGg-UAGACG- -5'
miRNA: 3'- cAugUCg-----UGACa---CCGACCGGuAGACG- -5'
miRNA: 3'- -CAUGuCGUGACa-CCGACCGgua---GACG- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 3148 | 3' | -55 | NC_001499.1 | + | 3345 | 1.12 | 1.6e-05 |
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Target: 5'- aGUACAGCACUGUGGCUGGCCAUCUGCu -3' miRNA: 3'- -CAUGUCGUGACACCGACCGGUAGACG- -5' |
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| 3148 | 3' | -55 | NC_001499.1 | + | 3505 | 0.74 | 0.03001 |
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Target: 5'- -gGCAGCuggcccacuggagGCUGUGGCagGGCagAUCUGCa -3' miRNA: 3'- caUGUCG-------------UGACACCGa-CCGg-UAGACG- -5' |
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| 3148 | 3' | -55 | NC_001499.1 | + | 2639 | 0.7 | 0.067935 |
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Target: 5'- uUugGGagucaaGCUGggagGGCUGGCUuUCUGCu -3' miRNA: 3'- cAugUCg-----UGACa---CCGACCGGuAGACG- -5' |
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| 3148 | 3' | -55 | NC_001499.1 | + | 3330 | 0.67 | 0.102965 |
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Target: 5'- aGUGCuGUACUGgaGGCUGGCaagaacCUGUa -3' miRNA: 3'- -CAUGuCGUGACa-CCGACCGgua---GACG- -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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