miRNA: 3'- gAUcGCGUGG--UGaaa----AGUGAUCCACA- -5'
miRNA: 3'- -GAUCGCGugGUgaaa---AGuGAUCCACA- -5'
miRNA: 3'- -GAUCGCGUGgUGAaaagUGAUCCAca -5'
miRNA: 3'- -GAUCGCGUGGUGAAAAGUGAUCCACA- -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 | |||||||
| 29109 | 5' | -49.7 | NC_006146.1 | + | 80860 | 0.66 | 0.99796 |
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Target: 5'- aUAaCGCACCccGCggugccaUCACUGGGUGUu -3' miRNA: 3'- gAUcGCGUGG--UGaaa----AGUGAUCCACA- -5' |
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| 29109 | 5' | -49.7 | NC_006146.1 | + | 99803 | 0.66 | 0.996572 |
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Target: 5'- gCUAGUGCugCAaugggccUCuCUGGGUGUa -3' miRNA: 3'- -GAUCGCGugGUgaaa---AGuGAUCCACA- -5' |
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| 29109 | 5' | -49.7 | NC_006146.1 | + | 59918 | 0.66 | 0.996572 |
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Target: 5'- gCUGGUGCGCgGCUacgaGCUGGGUc- -3' miRNA: 3'- -GAUCGCGUGgUGAaaagUGAUCCAca -5' |
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| 29109 | 5' | -49.7 | NC_006146.1 | + | 133460 | 1.08 | 0.014268 |
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Target: 5'- gCUAGCGCACCACUUUUCACUAGGUGUc -3' miRNA: 3'- -GAUCGCGUGGUGAAAAGUGAUCCACA- -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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