miRNA: 3'- -GGAGGAGAUCA------UGa--UGGcuAAGCUGa -5'
miRNA: 3'- -GGaGGAGAUCAUGa--UGGCuaaGCuGa -5'
miRNA: 3'- -GGAgGAGAUCA---UGAUGGcuAAGCUga -5'
miRNA: 3'- -GGAGGAGau-CAUGAugGCuaa---GCUGa -5'
miRNA: 3'- -GGAGGAGAUCAUGAUGGCUAAGCUGA- -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 | |||||||
| 25938 | 3' | -49.1 | NC_005337.1 | + | 23707 | 0.66 | 0.998358 |
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Target: 5'- uCCUCUUCUGGUucaaggGCgagACC--UUCGACa -3' miRNA: 3'- -GGAGGAGAUCA------UGa--UGGcuAAGCUGa -5' |
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| 25938 | 3' | -49.1 | NC_005337.1 | + | 65981 | 0.67 | 0.997193 |
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Target: 5'- aCCgCCUCUGGUGCgagGCCGug-CGuCc -3' miRNA: 3'- -GGaGGAGAUCAUGa--UGGCuaaGCuGa -5' |
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| 25938 | 3' | -49.1 | NC_005337.1 | + | 38770 | 0.67 | 0.996087 |
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Target: 5'- uCCUgCUCUGGUucaACUACCucUUCGGu- -3' miRNA: 3'- -GGAgGAGAUCA---UGAUGGcuAAGCUga -5' |
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| 25938 | 3' | -49.1 | NC_005337.1 | + | 94992 | 0.68 | 0.993779 |
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Target: 5'- uCCUCCUCcgcGUACUugCGcgacagCGGCg -3' miRNA: 3'- -GGAGGAGau-CAUGAugGCuaa---GCUGa -5' |
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| 25938 | 3' | -49.1 | NC_005337.1 | + | 116237 | 1.1 | 0.011186 |
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Target: 5'- cCCUCCUCUAGUACUACCGAUUCGACUu -3' miRNA: 3'- -GGAGGAGAUCAUGAUGGCUAAGCUGA- -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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