miRNA: 3'- -UGGUAGACucUaUCaGGACU----UGGCGG- -5'
miRNA: 3'- uGGUAGAC--------------UCUAuCAGGa--CUUGGCGg -5'
miRNA: 3'- -UGGUAGACUCUAUCaGGACuUGGCGg -5'
miRNA: 3'- -UGGUAGACUCUAUCAGGACUUGGCGG- -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 | |||||||
| 1178 | 5' | -51.7 | NC_001132.2 | + | 99900 | 0.67 | 0.979731 |
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Target: 5'- cACCAUCUGuuAcAG-CCUGGguauAUCGCCa -3' miRNA: 3'- -UGGUAGACucUaUCaGGACU----UGGCGG- -5' |
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| 1178 | 5' | -51.7 | NC_001132.2 | + | 9943 | 0.68 | 0.964974 |
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Target: 5'- uCCAUCUGgcgacguguuuaggGGAU-GUCCcagGAACCGCa -3' miRNA: 3'- uGGUAGAC--------------UCUAuCAGGa--CUUGGCGg -5' |
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| 1178 | 5' | -51.7 | NC_001132.2 | + | 118330 | 0.74 | 0.75247 |
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Target: 5'- uACCGUUUGAGAUGG-CUUGuACCGUa -3' miRNA: 3'- -UGGUAGACUCUAUCaGGACuUGGCGg -5' |
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| 1178 | 5' | -51.7 | NC_001132.2 | + | 158577 | 1.13 | 0.004259 |
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Target: 5'- gACCAUCUGAGAUAGUCCUGAACCGCCa -3' miRNA: 3'- -UGGUAGACUCUAUCAGGACUUGGCGG- -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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