miRNA: 3'- aUGUGCAGGGCGCG---------------CGUAuGgCGCGA- -5'
miRNA: 3'- -AUGugCAgGGCG-------------CGCGUAUGGCGCGa -5'
miRNA: 3'- -AUGUGCAGGGCGCGCGUaugGCGCGa -5'
miRNA: 3'- -AUGUGCAGGGCGCGCGUAUGGCGCGA- -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 | |||||||
| 12700 | 5' | -59.5 | NC_003349.1 | + | 42544 | 0.66 | 0.719405 |
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Target: 5'- gGCACGUUCCGCGCuguucauuauuaucuGCAU-CgGUGUUg -3' miRNA: 3'- aUGUGCAGGGCGCG---------------CGUAuGgCGCGA- -5' |
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| 12700 | 5' | -59.5 | NC_003349.1 | + | 100489 | 0.66 | 0.694579 |
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Target: 5'- uUGCugGUgUCGCcgaacucgugaacGUGUAUACCGUGCa -3' miRNA: 3'- -AUGugCAgGGCG-------------CGCGUAUGGCGCGa -5' |
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| 12700 | 5' | -59.5 | NC_003349.1 | + | 38895 | 0.69 | 0.524667 |
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Target: 5'- gUACACGUCCCGUGUGUG---UGUGCg -3' miRNA: 3'- -AUGUGCAGGGCGCGCGUaugGCGCGa -5' |
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| 12700 | 5' | -59.5 | NC_003349.1 | + | 37445 | 1.05 | 0.001961 |
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Target: 5'- aUACACGUCCCGCGCGCAUACCGCGCUc -3' miRNA: 3'- -AUGUGCAGGGCGCGCGUAUGGCGCGA- -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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