miRNA: 3'- gCC-GUCUUCUUUCGuUCCCa-GUGGUg -5'
miRNA: 3'- gCCGUCUUc----UUUCGU---------------UC-CCAGUGGUG- -5'
miRNA: 3'- -GCCGUCUUCU---------UUCGUUCCcagUGG--UG- -5'
miRNA: 3'- -GCCGUCUUCu-U-------------UCGUUCCC--AG-UGGUG- -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 |
| Predicted miRNA align pattern | |||||||
| 8935 | 3' | -52.5 | NC_002484.1 | + | 1398 | 0.66 | 0.853858 |
|
Target: 5'- gGGcCAGGAGGAAGUcAGGGaaUACCGa -3' miRNA: 3'- gCC-GUCUUCUUUCGuUCCCa-GUGGUg -5' |
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| 8935 | 3' | -52.5 | NC_002484.1 | + | 10620 | 0.71 | 0.583019 |
|
Target: 5'- aGGCGGAAccgccGGAGCGcugaaugguugcgguAGaGGUCACCACa -3' miRNA: 3'- gCCGUCUUc----UUUCGU---------------UC-CCAGUGGUG- -5' |
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| 8935 | 3' | -52.5 | NC_002484.1 | + | 33811 | 0.66 | 0.853858 |
|
Target: 5'- gCGGCAGGAGAagggauuguGAGCAAGGa--ACUgaACa -3' miRNA: 3'- -GCCGUCUUCU---------UUCGUUCCcagUGG--UG- -5' |
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| 8935 | 3' | -52.5 | NC_002484.1 | + | 36492 | 0.67 | 0.79689 |
|
Target: 5'- gCGGCAGGAGucAuccgcuaucguucAGCGGGGGagUCuGCCACc -3' miRNA: 3'- -GCCGUCUUCu-U-------------UCGUUCCC--AG-UGGUG- -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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