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miRNA: 3'- cuaUGCGUGGCUUca------GUGAGCc-UGCC- -5'
miRNA: 3'- -CUAUGCG-----UGGCUUCAGUGaGC-CUGCC- -5'
miRNA: 3'- -CUAUGCGUGGCUUCAGUGAGCCUGCC- -5'
Results 1 - 3 of 3 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position |
R_P_ratio#
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P value |
| Predicted miRNA align pattern | |||||||
| 21165 | 5' | -52.6 | NC_004777.1 | + | 25882 | 0.67 | 0.738413 |
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Target: 5'- --aACGCACCGGAugcguaagCACUCGcaGCGGa -3' miRNA: 3'- cuaUGCGUGGCUUca------GUGAGCc-UGCC- -5' |
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| 21165 | 5' | -52.6 | NC_004777.1 | + | 12521 | 0.73 | 0.365241 |
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Target: 5'- gGAUGCGCuggaaGCCGAGGUUGCaCGaGGCGGu -3' miRNA: 3'- -CUAUGCG-----UGGCUUCAGUGaGC-CUGCC- -5' |
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| 21165 | 5' | -52.6 | NC_004777.1 | + | 12557 | 1.11 | 0.001095 |
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Target: 5'- aGAUACGCACCGAAGUCACUCGGACGGu -3' miRNA: 3'- -CUAUGCGUGGCUUCAGUGAGCCUGCC- -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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