miRNA: 3'- -GACGGGu----Ca--GUG-----------UUUCCCUCCUGAac -5'
miRNA: 3'- gaCGGGUC--------AGugUuUCCCUCCUGAac -5'
miRNA: 3'- gaCGGGUC--------AGugUuUCCCUCCUGAac -5'
miRNA: 3'- -GACGGGUCAGUGUUUCCCUCCUGAAC- -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 | |||||||
| 3236 | 5' | -53.6 | NC_001514.1 | + | 6395 | 0.67 | 0.21669 |
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Target: 5'- aCUGCCCucuuuGgagCGCcaugugacuguAAAGGGGGGACUc- -3' miRNA: 3'- -GACGGGu----Ca--GUG-----------UUUCCCUCCUGAac -5' |
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| 3236 | 5' | -53.6 | NC_001514.1 | + | 88 | 0.68 | 0.197332 |
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Target: 5'- -cGCCCGGggcaugcuUUugGcGGGGAGGGCUg- -3' miRNA: 3'- gaCGGGUC--------AGugUuUCCCUCCUGAac -5' |
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| 3236 | 5' | -53.6 | NC_001514.1 | + | 8409 | 0.68 | 0.197332 |
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Target: 5'- -cGCCCGGggcaugcuUUugGcGGGGAGGGCUg- -3' miRNA: 3'- gaCGGGUC--------AGugUuUCCCUCCUGAac -5' |
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| 3236 | 5' | -53.6 | NC_001514.1 | + | 6345 | 1.09 | 8.8e-05 |
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Target: 5'- uCUGCCCAGUCACAAAGGGAGGACUUGg -3' miRNA: 3'- -GACGGGUCAGUGUUUCCCUCCUGAAC- -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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