miRNA: 3'- -UAGUCGGA--CGCUAGACGU----CCauaagc -5'
miRNA: 3'- -UAGuCGGACGC-UAGa------CGUCCAU-AAGC- -5'
miRNA: 3'- -UAGUCGGACG-----CUAGa---CGUCCauAAGC- -5'
miRNA: 3'- -UAGUCGGACGCUAGACGUCCAUAAGC- -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 | |||||||
| 26123 | 5' | -52.8 | NC_005342.2 | + | 3762 | 0.67 | 0.734488 |
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Target: 5'- gAUCGGCCUucGCGAUCUGCGcagcGGa----- -3' miRNA: 3'- -UAGUCGGA--CGCUAGACGU----CCauaagc -5' |
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| 26123 | 5' | -52.8 | NC_005342.2 | + | 811 | 0.67 | 0.689696 |
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Target: 5'- gGUC-GCCUGCGcGUCgcucggcGCGGGUGuUUCGa -3' miRNA: 3'- -UAGuCGGACGC-UAGa------CGUCCAU-AAGC- -5' |
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| 26123 | 5' | -52.8 | NC_005342.2 | + | 1496 | 0.69 | 0.586538 |
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Target: 5'- aGUCGGCCUGCagcguGAUCgucaGCGGGacUUCGu -3' miRNA: 3'- -UAGUCGGACG-----CUAGa---CGUCCauAAGC- -5' |
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| 26123 | 5' | -52.8 | NC_005342.2 | + | 416 | 1.08 | 0.001453 |
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Target: 5'- gAUCAGCCUGCGAUCUGCAGGUAUUCGa -3' miRNA: 3'- -UAGUCGGACGCUAGACGUCCAUAAGC- -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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