miRNA: 3'- -GGCGCGGuGGUaa-------UCUGUaGUUAGUa -5'
miRNA: 3'- -GGCGCGGUGguaaUCUGU------AGUUAGua -5'
miRNA: 3'- -GGCGCGGuGGUaa---UCUGUAGUUaGUa -5'
miRNA: 3'- gGCGCGGUGGUaau--CUGUAGU-UAGua -5'
miRNA: 3'- -GGCGCGGUGGUAAUCUGUAGUUAGUA- -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 | |||||||
| 326 | 5' | -49.4 | AC_000010.1 | + | 18021 | 0.66 | 0.878428 |
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Target: 5'- uCCGCGCC-CCGaucuggaggAGACAcUAGUCAc -3' miRNA: 3'- -GGCGCGGuGGUaa-------UCUGUaGUUAGUa -5' |
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| 326 | 5' | -49.4 | AC_000010.1 | + | 18592 | 0.68 | 0.803291 |
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Target: 5'- cCCGCGCCAC----AGACAccuacuUCAAUCu- -3' miRNA: 3'- -GGCGCGGUGguaaUCUGU------AGUUAGua -5' |
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| 326 | 5' | -49.4 | AC_000010.1 | + | 16685 | 0.69 | 0.737817 |
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Target: 5'- cCCGUGCCuCCAcgcagAGGCAUCAAgCGa -3' miRNA: 3'- -GGCGCGGuGGUaa---UCUGUAGUUaGUa -5' |
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| 326 | 5' | -49.4 | AC_000010.1 | + | 17468 | 0.69 | 0.714839 |
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Target: 5'- gCGCGCCGCCGccuguGGCGUCGcAUCc- -3' miRNA: 3'- gGCGCGGUGGUaau--CUGUAGU-UAGua -5' |
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| 326 | 5' | -49.4 | AC_000010.1 | + | 27526 | 1.09 | 0.002186 |
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Target: 5'- gCCGCGCCACCAUUAGACAUCAAUCAUa -3' miRNA: 3'- -GGCGCGGUGGUAAUCUGUAGUUAGUA- -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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