miRNA: 3'- -CAGGUuUuaGaCGACGGuaCGGUGCu -5'
miRNA: 3'- caGGUUUUaGACGACGGUA-----------CGGUGcu -5'
miRNA: 3'- -CAGGUUUUAGACGACGGUACGGUGCU- -5'
Results 1 - 3 of 3 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 | |||||||
| 2500 | 3' | -51.5 | NC_001454.1 | + | 3127 | 0.66 | 0.764233 |
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Target: 5'- gGUCCGuAcgCaGCUGCUcgGUCACGu -3' miRNA: 3'- -CAGGUuUuaGaCGACGGuaCGGUGCu -5' |
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| 2500 | 3' | -51.5 | NC_001454.1 | + | 23471 | 0.71 | 0.442813 |
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Target: 5'- -aCCAAAA-CUGCUGCCAUcaucauuuuucGCCGCu- -3' miRNA: 3'- caGGUUUUaGACGACGGUA-----------CGGUGcu -5' |
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| 2500 | 3' | -51.5 | NC_001454.1 | + | 3503 | 1.1 | 0.000945 |
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Target: 5'- aGUCCAAAAUCUGCUGCCAUGCCACGAg -3' miRNA: 3'- -CAGGUUUUAGACGACGGUACGGUGCU- -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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