miRNA: 3'- -GGGACUUUUGCAGAAAAGGCGGCGGU- -5'
miRNA: 3'- gGGACUu-UUGCAG------------AAAAGGCGGcGGU- -5'
miRNA: 3'- gGGACUUUUGCAGaaaaggCgGCGGU- -5'
miRNA: 3'- -GGGa-----CUUUUGCAGa------------AAAggCGGCGGu -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 | |||||||
| 1280 | 3' | -50.8 | NC_001317.1 | + | 4358 | 1.12 | 0.001004 |
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Target: 5'- aCCCUGAAAACGUCUUUUCCGCCGCCAc -3' miRNA: 3'- -GGGACUUUUGCAGAAAAGGCGGCGGU- -5' |
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| 1280 | 3' | -50.8 | NC_001317.1 | + | 12329 | 0.69 | 0.636928 |
|
Target: 5'- aCCUGAccGGCGUCcggcacuggcagUUUUCCGCCuCCGu -3' miRNA: 3'- gGGACUu-UUGCAG------------AAAAGGCGGcGGU- -5' |
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| 1280 | 3' | -50.8 | NC_001317.1 | + | 16761 | 0.67 | 0.729893 |
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Target: 5'- gCCUGAGAACGUCgguacaG-CGCCAg -3' miRNA: 3'- gGGACUUUUGCAGaaaaggCgGCGGU- -5' |
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| 1280 | 3' | -50.8 | NC_001317.1 | + | 6692 | 0.66 | 0.811668 |
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Target: 5'- gCCCggcucgGGGAGCGUUcguuaaccggcggUUUuuGCCGCCu -3' miRNA: 3'- -GGGa-----CUUUUGCAGa------------AAAggCGGCGGu -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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