miRNA: 3'- gcuCCUUAUGCaacAGCGGCuuGCGG- -5'
miRNA: 3'- -GCUC-CUu----AUGCA---ACA---GCGGCU--UGCGG- -5'
miRNA: 3'- gCUCCuuaUGCAACAG---CGGCUUGcGG- -5'
miRNA: 3'- -GCUCCUUAUGCAACAGCGGCUUGCGG- -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 | |||||||
| 11287 | 3' | -51 | NC_003083.1 | + | 44672 | 0.66 | 0.990668 |
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Target: 5'- --cGGAAUGCGa--UCGCCGu-UGCCg -3' miRNA: 3'- gcuCCUUAUGCaacAGCGGCuuGCGG- -5' |
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| 11287 | 3' | -51 | NC_003083.1 | + | 74245 | 0.68 | 0.963454 |
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Target: 5'- gCGGGaGAucgguUGCGUucuUGUgaaCGCCGAcgACGCCg -3' miRNA: 3'- -GCUC-CUu----AUGCA---ACA---GCGGCU--UGCGG- -5' |
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| 11287 | 3' | -51 | NC_003083.1 | + | 110227 | 0.71 | 0.868503 |
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Target: 5'- gGAGGug-ACGUUGUCggaGCCGAGCaCUa -3' miRNA: 3'- gCUCCuuaUGCAACAG---CGGCUUGcGG- -5' |
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| 11287 | 3' | -51 | NC_003083.1 | + | 58023 | 1.13 | 0.004533 |
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Target: 5'- cCGAGGAAUACGUUGUCGCCGAACGCCu -3' miRNA: 3'- -GCUCCUUAUGCAACAGCGGCUUGCGG- -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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