miRNA: 3'- gaCGGGC---ACGGGGauaCCCGGG--UCGa -5'
miRNA: 3'- gaCGGGca----CgGGGAUACCCGGGuCGa -5'
miRNA: 3'- -GACGG-GCaCGGGGAUac--CC-GGGUCGA- -5'
miRNA: 3'- -GACGGGCACGGGGAUACCCGGGUCGA- -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 | |||||||
| 13014 | 5' | -63.2 | NC_003390.1 | + | 37871 | 0.66 | 0.272665 |
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Target: 5'- -cGCCCGgguUGCCUUgg-GGGCCUugAGCa -3' miRNA: 3'- gaCGGGC---ACGGGGauaCCCGGG--UCGa -5' |
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| 13014 | 5' | -63.2 | NC_003390.1 | + | 38159 | 0.68 | 0.186001 |
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Target: 5'- -gGCCCcuggaaGgCCCUGUGGGCCCuGUa -3' miRNA: 3'- gaCGGGca----CgGGGAUACCCGGGuCGa -5' |
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| 13014 | 5' | -63.2 | NC_003390.1 | + | 8858 | 0.68 | 0.186001 |
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Target: 5'- uCUGCCgUG-GCCCCUAcacaGGcCCCAGCUg -3' miRNA: 3'- -GACGG-GCaCGGGGAUac--CC-GGGUCGA- -5' |
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| 13014 | 5' | -63.2 | NC_003390.1 | + | 5692 | 1.07 | 0.00018 |
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Target: 5'- aCUGCCCGUGCCCCUAUGGGCCCAGCUc -3' miRNA: 3'- -GACGGGCACGGGGAUACCCGGGUCGA- -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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