miRNA: 3'- cUGCG---AUAGUUGCUGG------UCUAGUUUCU- -5'
miRNA: 3'- cUGC-GAUAGUUG------CUGGUCUa----GUUUCU- -5'
miRNA: 3'- cUGCGa-----UA-GUUGCUGGUCUAGUuuCU- -5'
miRNA: 3'- -CUGCGAUAGUUGCUGGUCUAGUUUCU- -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 | |||||||
| 28231 | 5' | -47 | NC_005893.1 | + | 5243 | 0.66 | 0.975774 |
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Target: 5'- aACGCaucUGUUGACGAUUuucaaaAGAUCAAGGAu -3' miRNA: 3'- cUGCG---AUAGUUGCUGG------UCUAGUUUCU- -5' |
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| 28231 | 5' | -47 | NC_005893.1 | + | 8572 | 0.66 | 0.969354 |
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Target: 5'- uGCGuCUGUCAGCauuaguGACCAGAaguuaCGGAGAc -3' miRNA: 3'- cUGC-GAUAGUUG------CUGGUCUa----GUUUCU- -5' |
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| 28231 | 5' | -47 | NC_005893.1 | + | 31752 | 0.67 | 0.95305 |
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Target: 5'- cGCGCguuuggAUaCAACGAUCAGGUUAuuGAa -3' miRNA: 3'- cUGCGa-----UA-GUUGCUGGUCUAGUuuCU- -5' |
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| 28231 | 5' | -47 | NC_005893.1 | + | 5305 | 1.1 | 0.004319 |
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Target: 5'- gGACGCUAUCAACGACCAGAUCAAAGAc -3' miRNA: 3'- -CUGCGAUAGUUGCUGGUCUAGUUUCU- -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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