miRNA: 3'- cUCGUG--UUGGUCGUG------------CCGuUGG-GACC- -5'
miRNA: 3'- cUCGUGUugGUCGugCCgUUGG-----GACC- -5'
miRNA: 3'- cUC-GU--GUUGGUCGUGCCGuugGGACC- -5'
miRNA: 3'- -CUCGUGUUGGUCGUGCCGUUGGGACC- -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 | |||||||
| 6005 | 3' | -56 | NC_001809.1 | + | 8230 | 0.66 | 0.204425 |
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Target: 5'- cGGUAUggAGCCAGCACcuugaacacgcaGGCcGCCgCUGGg -3' miRNA: 3'- cUCGUG--UUGGUCGUG------------CCGuUGG-GACC- -5' |
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| 6005 | 3' | -56 | NC_001809.1 | + | 9079 | 0.67 | 0.198343 |
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Target: 5'- uGGUACAugUGGCugGGgAGCCgcuucCUGGa -3' miRNA: 3'- cUCGUGUugGUCGugCCgUUGG-----GACC- -5' |
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| 6005 | 3' | -56 | NC_001809.1 | + | 6997 | 0.68 | 0.170254 |
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Target: 5'- uGGaCAucCAGCCGGCACGGU---CCUGGg -3' miRNA: 3'- cUC-GU--GUUGGUCGUGCCGuugGGACC- -5' |
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| 6005 | 3' | -56 | NC_001809.1 | + | 955 | 1.1 | 0.000065 |
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Target: 5'- gGAGCACAACCAGCACGGCAACCCUGGu -3' miRNA: 3'- -CUCGUGUUGGUCGUGCCGUUGGGACC- -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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