miRNA: 3'- cucUGGGUaGCUGGCUUCGGUAagCA- -5'
miRNA: 3'- -CUCUGGgUAgC-UGGCUUCGGUAAGca -5'
miRNA: 3'- cUCUGGGUAGCUG-------GCUUCGGU-AAGCa -5'
miRNA: 3'- -CUCUGGGUAGCUGGCUUCGGUAAGCA- -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 | |||||||
| 21014 | 5' | -53.5 | NC_004735.1 | + | 45635 | 0.66 | 0.953239 |
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Target: 5'- --aGCCCA-CGACUGAAGUCGUggGUa -3' miRNA: 3'- cucUGGGUaGCUGGCUUCGGUAagCA- -5' |
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| 21014 | 5' | -53.5 | NC_004735.1 | + | 46540 | 0.67 | 0.934897 |
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Target: 5'- uGGGAUC-AUgGcACCGGAGCCAUUCa- -3' miRNA: 3'- -CUCUGGgUAgC-UGGCUUCGGUAAGca -5' |
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| 21014 | 5' | -53.5 | NC_004735.1 | + | 126226 | 0.68 | 0.878286 |
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Target: 5'- aGGAUCCGUCGACuggucuuCGAAGUCGuUUCGa -3' miRNA: 3'- cUCUGGGUAGCUG-------GCUUCGGU-AAGCa -5' |
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| 21014 | 5' | -53.5 | NC_004735.1 | + | 72357 | 1.07 | 0.005512 |
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Target: 5'- cGAGACCCAUCGACCGAAGCCAUUCGUu -3' miRNA: 3'- -CUCUGGGUAGCUGGCUUCGGUAAGCA- -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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