miRNA: 3'- aAGCguua---GGCGCaUAUGUGAGGUUu -5'
miRNA: 3'- aaGCGUUAGGC-GC-AUAUGUGa------GGUUu -5'
miRNA: 3'- aAGCGUU--------------AGGCGCAUAUGUGa---GguUU- -5'
miRNA: 3'- -AAGCGUUAGGCGCAUAUGUGAGGUUU- -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 | |||||||
| 27925 | 5' | -49.8 | NC_005886.2 | + | 36483 | 0.67 | 0.869565 |
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Target: 5'- aUCGagaaugaCCGCG-AUGCGCUCCGAu -3' miRNA: 3'- aAGCguua---GGCGCaUAUGUGAGGUUu -5' |
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| 27925 | 5' | -49.8 | NC_005886.2 | + | 39241 | 0.67 | 0.851899 |
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Target: 5'- -gCGCAGUCCGuCGaUAUGCGCcacguugCCAAu -3' miRNA: 3'- aaGCGUUAGGC-GC-AUAUGUGa------GGUUu -5' |
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| 27925 | 5' | -49.8 | NC_005886.2 | + | 25682 | 0.69 | 0.768227 |
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Target: 5'- cUCGCAGcgagcgaggcguauUCCGCGUAUGCGCguugCguGAu -3' miRNA: 3'- aAGCGUU--------------AGGCGCAUAUGUGa---GguUU- -5' |
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| 27925 | 5' | -49.8 | NC_005886.2 | + | 13680 | 1.04 | 0.005261 |
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Target: 5'- gUUCGCAAUCCGCGUAUACACUCCAAAc -3' miRNA: 3'- -AAGCGUUAGGCGCAUAUGUGAGGUUU- -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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