miRNA: 3'- -GAGGA--GACUUCGGCC-AAGGGg--------UUGGa -5'
miRNA: 3'- gAGGAGACUUCGGCCaaggggUUGGa -5'
miRNA: 3'- -GAGGAGa-----CUUCGgCCA-------AGGGGUUGGa -5'
miRNA: 3'- gAGGAGac-UUCG-GCCaAGGGGUUGGa -5'
miRNA: 3'- -GAGGAGACUUCGGCCAAGGGGUUGGA- -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 | |||||||
| 21020 | 5' | -56.4 | NC_004735.1 | + | 119430 | 0.67 | 0.822199 |
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Target: 5'- gCUCUUacCUGAAGCCGGaUUCCUauuauaagaAACCa -3' miRNA: 3'- -GAGGA--GACUUCGGCC-AAGGGg--------UUGGa -5' |
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| 21020 | 5' | -56.4 | NC_004735.1 | + | 123365 | 0.67 | 0.822199 |
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Target: 5'- aUCUUCUGAAGCCGGgaaaa-GACCg -3' miRNA: 3'- gAGGAGACUUCGGCCaaggggUUGGa -5' |
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| 21020 | 5' | -56.4 | NC_004735.1 | + | 129503 | 0.67 | 0.803689 |
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Target: 5'- uCUCUUCcuggcgGGAGCgGGUucaugcuUCCCCAAUCa -3' miRNA: 3'- -GAGGAGa-----CUUCGgCCA-------AGGGGUUGGa -5' |
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| 21020 | 5' | -56.4 | NC_004735.1 | + | 34222 | 0.68 | 0.776996 |
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Target: 5'- uUCCUUggcGAGCgCGGcUCCCCGAUCg -3' miRNA: 3'- gAGGAGac-UUCG-GCCaAGGGGUUGGa -5' |
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| 21020 | 5' | -56.4 | NC_004735.1 | + | 89939 | 1.07 | 0.002834 |
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Target: 5'- cCUCCUCUGAAGCCGGUUCCCCAACCUc -3' miRNA: 3'- -GAGGAGACUUCGGCCAAGGGGUUGGA- -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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