miRNA: 3'- aGGa---CCCg-CAGC-UCCAGGa-----GCCCCAU- -5'
miRNA: 3'- -AGGACcCGC---AGCUCCaGGAGCC-CCau -5'
miRNA: 3'- -AGGACCCGCAGCUCCAGGAGCCCCAU- -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 | |||||||
| 16299 | 5' | -61.9 | NC_004084.1 | + | 18983 | 0.67 | 0.356662 |
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Target: 5'- gCCggcgGGGaaGUCGuAGGUCCcgcuggCGGGGUGg -3' miRNA: 3'- aGGa---CCCg-CAGC-UCCAGGa-----GCCCCAU- -5' |
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| 16299 | 5' | -61.9 | NC_004084.1 | + | 35528 | 0.67 | 0.340724 |
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Target: 5'- aUCCUGcGCGugaUCGAGGaCCUCGGcGGc- -3' miRNA: 3'- -AGGACcCGC---AGCUCCaGGAGCC-CCau -5' |
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| 16299 | 5' | -61.9 | NC_004084.1 | + | 35135 | 1.06 | 0.000405 |
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Target: 5'- aUCCUGGGCGUCGAGGUCCUCGGGGUAc -3' miRNA: 3'- -AGGACCCGCAGCUCCAGGAGCCCCAU- -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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