miRNA: 3'- aGUCaGUCcCGGCCG----GGuCCUCGGac -5'
miRNA: 3'- aGUCAG-UCCCGgCCGG-------------GUCCucGGAC- -5'
miRNA: 3'- agucAGUCCCGG--CCGGGUC----CUCGGac -5'
miRNA: 3'- -AGUCAGUCCCGGCCGGGUCCUCGGAC- -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 | |||||||
| 2281 | 5' | -63.2 | NC_001407.1 | + | 7153 | 0.66 | 0.064551 |
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Target: 5'- cCAGcCAGcGCCGGCacagCCuGGAGCCa- -3' miRNA: 3'- aGUCaGUCcCGGCCG----GGuCCUCGGac -5' |
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| 2281 | 5' | -63.2 | NC_001407.1 | + | 985 | 0.68 | 0.042508 |
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Target: 5'- aCAGUCaAGGGCgGGCCagggcaugcggguCAGGcuCCUGg -3' miRNA: 3'- aGUCAG-UCCCGgCCGG-------------GUCCucGGAC- -5' |
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| 2281 | 5' | -63.2 | NC_001407.1 | + | 2069 | 0.68 | 0.041298 |
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Target: 5'- ---uUCGGGGCCguGGCCCGGcccuGAGCCa- -3' miRNA: 3'- agucAGUCCCGG--CCGGGUC----CUCGGac -5' |
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| 2281 | 5' | -63.2 | NC_001407.1 | + | 1050 | 1.08 | 1.1e-05 |
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Target: 5'- gUCAGUCAGGGCCGGCCCAGGAGCCUGa -3' miRNA: 3'- -AGUCAGUCCCGGCCGGGUCCUCGGAC- -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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