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miRNA: 3'- -UCGGAAUCaGGG-------CGUG--UAGCCUAUUU- -5'
miRNA: 3'- -UCGG-------------AAUCa--GGGCGUGUaGCCUAUuu -5'
miRNA: 3'- -UCGGAAUCAGGGCGUGUAGCCUAUUU- -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 | |||||||
| 27736 | 5' | -51.8 | NC_005884.1 | + | 2637 | 0.66 | 0.79798 |
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Target: 5'- uAGCCUUAG-CCUcuugcugGCGCcuGUUGGAUAGGa -3' miRNA: 3'- -UCGGAAUCaGGG-------CGUG--UAGCCUAUUU- -5' |
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| 27736 | 5' | -51.8 | NC_005884.1 | + | 26914 | 0.67 | 0.755583 |
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Target: 5'- aAGCCaacuauuaauuuaUUAGgagCCUGCACAcCGGAUAc- -3' miRNA: 3'- -UCGG-------------AAUCa--GGGCGUGUaGCCUAUuu -5' |
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| 27736 | 5' | -51.8 | NC_005884.1 | + | 31601 | 1.06 | 0.002123 |
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Target: 5'- aAGCCUUAGUCCCGCACAUCGGAUAAAu -3' miRNA: 3'- -UCGGAAUCAGGGCGUGUAGCCUAUUU- -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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