miRNA: 3'- -AGG----CGCGAAGUUG--CAAUA-GAUAGUCc -5'
miRNA: 3'- aGGCGCGa--AGUUGCAAUA--GAUAGUCc -5'
miRNA: 3'- aGGCGcgAAGUUGCAAUAGA--------------UAGUCc -5'
miRNA: 3'- -AGGCGCGAAGUUGCAAUAGAUAGUCC- -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 | |||||||
| 27309 | 5' | -47.3 | NC_005856.1 | + | 64149 | 0.7 | 0.971167 |
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Target: 5'- uUCCuucaGUGCUUCAACuuGUUGUuCUGUCAGu -3' miRNA: 3'- -AGG----CGCGAAGUUG--CAAUA-GAUAGUCc -5' |
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| 27309 | 5' | -47.3 | NC_005856.1 | + | 9903 | 0.72 | 0.948021 |
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Target: 5'- cCUGCGCaccUCAACGUUAUgcUUGUCAGc -3' miRNA: 3'- aGGCGCGa--AGUUGCAAUA--GAUAGUCc -5' |
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| 27309 | 5' | -47.3 | NC_005856.1 | + | 81161 | 0.73 | 0.919409 |
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Target: 5'- gCCGCuuUUCAACGUUGUCUgggcgcgcgagcguAUCAGu -3' miRNA: 3'- aGGCGcgAAGUUGCAAUAGA--------------UAGUCc -5' |
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| 27309 | 5' | -47.3 | NC_005856.1 | + | 90998 | 1.12 | 0.008515 |
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Target: 5'- uUCCGCGCUUCAACGUUAUCUAUCAGGu -3' miRNA: 3'- -AGGCGCGAAGUUGCAAUAGAUAGUCC- -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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