miRNA: 3'- aAGUCACUGU--UCGaGCCUUuCCCUGa -5'
miRNA: 3'- -AAGUCACUGuUCGagCCUUUCCCUga -5'
miRNA: 3'- aagUCACUGUUCgAGCCu------UUCCCUGa -5'
miRNA: 3'- -AAGUCACUGUUCGAGCCUUUCCCUGA- -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 | |||||||
| 11858 | 5' | -52.1 | NC_003266.2 | + | 20200 | 0.66 | 0.695288 |
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Target: 5'- gUUGGUGGCGuuGGC-CGGGAuGGGAUa -3' miRNA: 3'- aAGUCACUGU--UCGaGCCUUuCCCUGa -5' |
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| 11858 | 5' | -52.1 | NC_003266.2 | + | 34367 | 0.7 | 0.465027 |
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Target: 5'- uUUCGGUGAC-GGCg-GGGGAGGGAa- -3' miRNA: 3'- -AAGUCACUGuUCGagCCUUUCCCUga -5' |
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| 11858 | 5' | -52.1 | NC_003266.2 | + | 31821 | 0.72 | 0.374146 |
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Target: 5'- --uGGUGACAGGgUCGGccagccuAAGGGACa -3' miRNA: 3'- aagUCACUGUUCgAGCCu------UUCCCUGa -5' |
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| 11858 | 5' | -52.1 | NC_003266.2 | + | 13389 | 1.06 | 0.001549 |
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Target: 5'- gUUCAGUGACAAGCUCGGAAAGGGACUg -3' miRNA: 3'- -AAGUCACUGUUCGAGCCUUUCCCUGA- -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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