miRNA: 3'- -GGaa----GCAGGCGGAC-GGcAAgGAGA----UG- -5'
miRNA: 3'- gGAAGcAGGCGGa-CGGCaa--GGAGaug -5'
miRNA: 3'- -GGAAGCAGGCGGACGgC-AAGGaGa--UG- -5'
miRNA: 3'- -GGAAGCAGGCGGACGGCAAGGAGAUG- -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 | |||||||
| 2816 | 5' | -55.3 | NC_001491.2 | + | 20315 | 0.66 | 0.933334 |
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Target: 5'- gCCggggcgCGUCCGCCUGgCCuUUgCUCUugagGCg -3' miRNA: 3'- -GGaa----GCAGGCGGAC-GGcAAgGAGA----UG- -5' |
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| 2816 | 5' | -55.3 | NC_001491.2 | + | 117654 | 0.66 | 0.922823 |
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Target: 5'- gCUUC-UCCGCCggGCCGgagcCCUCa-- -3' miRNA: 3'- gGAAGcAGGCGGa-CGGCaa--GGAGaug -5' |
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| 2816 | 5' | -55.3 | NC_001491.2 | + | 56829 | 0.67 | 0.905271 |
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Target: 5'- aUCUUUGUCCGUCUGUgGgUUCCcCgcgACg -3' miRNA: 3'- -GGAAGCAGGCGGACGgC-AAGGaGa--UG- -5' |
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| 2816 | 5' | -55.3 | NC_001491.2 | + | 124808 | 1.11 | 0.002672 |
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Target: 5'- aCCUUCGUCCGCCUGCCGUUCCUCUACc -3' miRNA: 3'- -GGAAGCAGGCGGACGGCAAGGAGAUG- -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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