miRNA: 3'- uuUCACc----UAAGAUUuUCUUCCGCGuc -5'
miRNA: 3'- -UUUCACCUaaGaUU----------UUCuuCCGCGUc -5'
miRNA: 3'- -UUUCACCUa--AGAU----UUUC-UUCCGCGUc -5'
miRNA: 3'- -UUUCACCUAAGAUUUUCUUCCGCGUC- -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 | |||||||
| 28213 | 5' | -46 | NC_005891.1 | + | 24065 | 0.66 | 0.982973 |
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Target: 5'- -cAGUGaacgaAUUCUGGcGGAAGGCGCu- -3' miRNA: 3'- uuUCACc----UAAGAUUuUCUUCCGCGuc -5' |
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| 28213 | 5' | -46 | NC_005891.1 | + | 39433 | 0.69 | 0.915115 |
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Target: 5'- cGAAGUGGGggCgGAggccgaugccAAGggGGCGCAc -3' miRNA: 3'- -UUUCACCUaaGaUU----------UUCuuCCGCGUc -5' |
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| 28213 | 5' | -46 | NC_005891.1 | + | 31935 | 0.71 | 0.808185 |
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Target: 5'- aGGAGUGGAagcUCUAucccAAGGcAAGGCGCAc -3' miRNA: 3'- -UUUCACCUa--AGAU----UUUC-UUCCGCGUc -5' |
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| 28213 | 5' | -46 | NC_005891.1 | + | 3574 | 1.07 | 0.006834 |
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Target: 5'- aAAAGUGGAUUCUAAAAGAAGGCGCAGu -3' miRNA: 3'- -UUUCACCUAAGAUUUUCUUCCGCGUC- -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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