miRNA: 3'- aUGcCAGCGCCAGAaGa---AGAGG-CUAC- -5'
miRNA: 3'- aUGCCAGCGCCAGA--AGaaGa----GGCUac -5'
miRNA: 3'- aUGCCAGCgCCAGA-AGAA--------GAGGCUac -5'
miRNA: 3'- aUgCCAgCGCCAGAAGAAGAG--GCUac -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 | |||||||
| 1979 | 3' | -53.6 | NC_001347.2 | + | 192162 | 0.66 | 0.986989 |
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Target: 5'- gGC-GUCGCGGUUUcCgccgUCUCCgGAUGa -3' miRNA: 3'- aUGcCAGCGCCAGAaGa---AGAGG-CUAC- -5' |
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| 1979 | 3' | -53.6 | NC_001347.2 | + | 134896 | 0.67 | 0.969318 |
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Target: 5'- gACGGUCGUGGUCUccUCggCccgugCCGGg- -3' miRNA: 3'- aUGCCAGCGCCAGA--AGaaGa----GGCUac -5' |
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| 1979 | 3' | -53.6 | NC_001347.2 | + | 37184 | 0.69 | 0.94786 |
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Target: 5'- gGCGGUCG-GGUCUgUCUUuuaugaugCUCCGAc- -3' miRNA: 3'- aUGCCAGCgCCAGA-AGAA--------GAGGCUac -5' |
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| 1979 | 3' | -53.6 | NC_001347.2 | + | 142456 | 0.75 | 0.656007 |
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Target: 5'- gGgGGUgGCGGUCUUCUUCUCggCGAg- -3' miRNA: 3'- aUgCCAgCGCCAGAAGAAGAG--GCUac -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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