miRNA: 3'- gCCG-UCCGUCUCuuCUCu--GUGUCgCC- -5'
miRNA: 3'- -GCCGUC--CGUCUCuuCUCugugUCGCC- -5'
miRNA: 3'- gCC-GUCCGUCUCUuCUCU-Gu----GUCGCc -5'
miRNA: 3'- -GCCGUCCGUCUCUUCUCUGUGUCGCC- -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 | |||||||
| 7596 | 5' | -55.7 | NC_001963.1 | + | 2562 | 0.67 | 0.102755 |
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Target: 5'- aGGCuGGGCGGGGccGGGugcUACAGgGGg -3' miRNA: 3'- gCCG-UCCGUCUCuuCUCu--GUGUCgCC- -5' |
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| 7596 | 5' | -55.7 | NC_001963.1 | + | 2464 | 0.67 | 0.092793 |
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Target: 5'- aCGGCGGaaGCGGGGggGGG----GGCGGg -3' miRNA: 3'- -GCCGUC--CGUCUCuuCUCugugUCGCC- -5' |
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| 7596 | 5' | -55.7 | NC_001963.1 | + | 3464 | 0.68 | 0.086668 |
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Target: 5'- aGGuCGGGCAGAGA-GAGGuCucgucCAGCGa -3' miRNA: 3'- gCC-GUCCGUCUCUuCUCU-Gu----GUCGCc -5' |
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| 7596 | 5' | -55.7 | NC_001963.1 | + | 2777 | 1.1 | 1.9e-05 |
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Target: 5'- aCGGCAGGCAGAGAAGAGACACAGCGGc -3' miRNA: 3'- -GCCGUCCGUCUCUUCUCUGUGUCGCC- -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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