miRNA: 3'- cUGCUG-GGCa---CCGGGUGU-----UGGACUAc -5'
miRNA: 3'- -CUGCu--GGGCaCC-GGGUGUUG-GACUac -5'
miRNA: 3'- -CUGCUGG-GCa----CCGGGUGu---UGGACUac -5'
miRNA: 3'- -CUGCuGGGCACCGgGUGUUGGACUac -5'
miRNA: 3'- -CUGCUGGGCACCGGGUGUUGGACUAC- -5'
Results 1 - 5 of 5 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 | |||||||
| 22565 | 5' | -57 | NC_005091.1 | + | 26769 | 0.66 | 0.637828 |
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Target: 5'- uGCGACgCCGcaccGGCUCGCGucuucGCCUGAUc -3' miRNA: 3'- cUGCUG-GGCa---CCGGGUGU-----UGGACUAc -5' |
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| 22565 | 5' | -57 | NC_005091.1 | + | 40502 | 0.66 | 0.605249 |
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Target: 5'- aGGCGuacCCCGaGGuCCCGCAGCuCUGGa- -3' miRNA: 3'- -CUGCu--GGGCaCC-GGGUGUUG-GACUac -5' |
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| 22565 | 5' | -57 | NC_005091.1 | + | 7849 | 0.67 | 0.540918 |
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Target: 5'- cGAUGACCuCGaagcaGGCCCAUgaguACCUGAa- -3' miRNA: 3'- -CUGCUGG-GCa----CCGGGUGu---UGGACUac -5' |
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| 22565 | 5' | -57 | NC_005091.1 | + | 38339 | 0.7 | 0.393373 |
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Target: 5'- cGGCG-UCCGUGGCaCACGGCUUGAa- -3' miRNA: 3'- -CUGCuGGGCACCGgGUGUUGGACUac -5' |
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| 22565 | 5' | -57 | NC_005091.1 | + | 13040 | 1.07 | 0.000952 |
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Target: 5'- gGACGACCCGUGGCCCACAACCUGAUGu -3' miRNA: 3'- -CUGCUGGGCACCGGGUGUUGGACUAC- -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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