miRNA: 3'- -GCCaaGCGA------GUGCC--UCGUCGGcAGGa -5'
miRNA: 3'- -GCCaa------GCGA-GuGCCUCGUCGGca-GGa -5'
miRNA: 3'- gCCAA----GCGAG----UGCCU---CGUCGGCAGga -5'
miRNA: 3'- -GCCa--AGCGAGUGCc-UCGUCGGCagga -5'
miRNA: 3'- -GCCAAGCGAGUGCCUCGUCGGCAGGA- -5'
Results 1 - 5 of 5 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 | |||||||
| 21338 | 5' | -58.7 | NC_004778.3 | + | 124082 | 0.66 | 0.788036 |
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Target: 5'- aCGGcgCGCUgaugcgCGCGGuuGGCGGCC-UCCg -3' miRNA: 3'- -GCCaaGCGA------GUGCC--UCGUCGGcAGGa -5' |
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| 21338 | 5' | -58.7 | NC_004778.3 | + | 34569 | 0.66 | 0.788036 |
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Target: 5'- aCGGgcacgccgCGCUgC-CGGAGCAGCCcggCCa -3' miRNA: 3'- -GCCaa------GCGA-GuGCCUCGUCGGca-GGa -5' |
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| 21338 | 5' | -58.7 | NC_004778.3 | + | 21181 | 0.66 | 0.778914 |
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Target: 5'- gGGUUaaagUGCUCgccgGCGGAcguGCAGCCGUUg- -3' miRNA: 3'- gCCAA----GCGAG----UGCCU---CGUCGGCAGga -5' |
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| 21338 | 5' | -58.7 | NC_004778.3 | + | 112472 | 0.67 | 0.731545 |
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Target: 5'- gCGGcagUCGCUCGCGccAGCGGCCGa--- -3' miRNA: 3'- -GCCa--AGCGAGUGCc-UCGUCGGCagga -5' |
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| 21338 | 5' | -58.7 | NC_004778.3 | + | 101287 | 1.07 | 0.001924 |
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Target: 5'- cCGGUUCGCUCACGGAGCAGCCGUCCUc -3' miRNA: 3'- -GCCAAGCGAGUGCCUCGUCGGCAGGA- -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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