miRNA: 3'- cACCUUguAA--------GGGCGAAGgCGUUACA- -5'
miRNA: 3'- -CACCUUGUAAgGGCGA--AGGCGuuaca -5'
miRNA: 3'- caCCUUGU-AAGGGCGaAGGCGUUaca -5'
miRNA: 3'- -CACCUUGUAAGGGCGAAGGCGUUACA- -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 | |||||||
| 6918 | 5' | -51.2 | NC_001875.2 | + | 113440 | 0.66 | 0.978819 |
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Target: 5'- aUGGGAguUUuggugaagCCCGUUUCgGCGGUGUa -3' miRNA: 3'- cACCUUguAA--------GGGCGAAGgCGUUACA- -5' |
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| 6918 | 5' | -51.2 | NC_001875.2 | + | 8890 | 0.69 | 0.922528 |
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Target: 5'- gGUGGAAUAUUgCCGCUccUCCGUu---- -3' miRNA: 3'- -CACCUUGUAAgGGCGA--AGGCGuuaca -5' |
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| 6918 | 5' | -51.2 | NC_001875.2 | + | 44144 | 0.69 | 0.922528 |
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Target: 5'- -cGGAGCGcUUUCCGUgUCCGCAAa-- -3' miRNA: 3'- caCCUUGU-AAGGGCGaAGGCGUUaca -5' |
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| 6918 | 5' | -51.2 | NC_001875.2 | + | 33412 | 1.07 | 0.008666 |
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Target: 5'- uGUGGAACAUUCCCGCUUCCGCAAUGUc -3' miRNA: 3'- -CACCUUGUAAGGGCGAAGGCGUUACA- -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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