miRNA: 3'- -UUGACu--UGUCGCGGgUGCGCCuAGuc -5'
miRNA: 3'- uugaCUUGUCGCG-GGUGCGCCua--GUC- -5'
miRNA: 3'- uUGACUUGUCGCGGGU---GC-GCCUaGUC- -5'
miRNA: 3'- -UUGACU---------------UGUCGCGGGUgCG--------CCUAGUc -5'
Results 21 - 24 of 24 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 23033 | 3' | -56.1 | NC_005178.1 | + | 7882 | 0.68 | 0.386083 |
|
Target: 5'- uGACUGugcGCGGCGCCgAUGCGG-UCc- -3' miRNA: 3'- -UUGACu--UGUCGCGGgUGCGCCuAGuc -5' |
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| 23033 | 3' | -56.1 | NC_005178.1 | + | 5544 | 0.72 | 0.224665 |
|
Target: 5'- ---gGAGCGGCGCgCCACGCGGuagaCGGu -3' miRNA: 3'- uugaCUUGUCGCG-GGUGCGCCua--GUC- -5' |
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| 23033 | 3' | -56.1 | NC_005178.1 | + | 4601 | 0.67 | 0.485827 |
|
Target: 5'- cACUGGGCGGCGUCCGgcuCGaUGGG-CAGg -3' miRNA: 3'- uUGACUUGUCGCGGGU---GC-GCCUaGUC- -5' |
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| 23033 | 3' | -56.1 | NC_005178.1 | + | 3995 | 0.72 | 0.246286 |
|
Target: 5'- gGGCUGAaacccuccgcuucguGCAGCGCCCAgGCuucguuggGGGUCAu -3' miRNA: 3'- -UUGACU---------------UGUCGCGGGUgCG--------CCUAGUc -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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