miRNA: 3'- gGAGU---UGGCCUU-----UCGACCuGUU--UGAC- -5'
miRNA: 3'- ggAGU-UGGCCUUUCGa--CCUGUU---UGAC- -5'
miRNA: 3'- -GGAGU--------UGGC-CUu--UCGACCUGUU----UGAc -5'
miRNA: 3'- -GGAGUUGGCCUUUCGACCUGUUUGAC- -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 | |||||||
| 7149 | 5' | -49.3 | NC_001895.1 | + | 11142 | 0.67 | 0.835296 |
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Target: 5'- aCUCAagcGCCGGGGucugcGGCUGGuCAAucAUUGa -3' miRNA: 3'- gGAGU---UGGCCUU-----UCGACCuGUU--UGAC- -5' |
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| 7149 | 5' | -49.3 | NC_001895.1 | + | 12561 | 0.67 | 0.82558 |
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Target: 5'- -aUCAaGCCGGAAGGUgccGGGCGGgucACUGu -3' miRNA: 3'- ggAGU-UGGCCUUUCGa--CCUGUU---UGAC- -5' |
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| 7149 | 5' | -49.3 | NC_001895.1 | + | 29104 | 0.68 | 0.795058 |
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Target: 5'- gCCUCAucguuccaGCCGuGAuuuAGCUGGACGGuuuuACUu -3' miRNA: 3'- -GGAGU--------UGGC-CUu--UCGACCUGUU----UGAc -5' |
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| 7149 | 5' | -49.3 | NC_001895.1 | + | 21188 | 1.12 | 0.001479 |
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Target: 5'- gCCUCAACCGGAAAGCUGGACAAACUGa -3' miRNA: 3'- -GGAGUUGGCCUUUCGACCUGUUUGAC- -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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