miRNA: 3'- -CCAgaCGCGUAGUccAACAUGCUuuu -5'
miRNA: 3'- cCAGa-CGCGUAguCCA--------ACAUGCUUUu -5'
miRNA: 3'- cCAGa-CGC-GUAGUCCAACA----------UGCUUuu -5'
miRNA: 3'- -CCAGACGCGUAGUCCAACAUGCUUUU- -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 | |||||||
| 8735 | 5' | -48.8 | NC_002331.1 | + | 118603 | 0.66 | 0.999388 |
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Target: 5'- cGGUaaGCGCGUCAa-UUGUGCGGc-- -3' miRNA: 3'- -CCAgaCGCGUAGUccAACAUGCUuuu -5' |
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| 8735 | 5' | -48.8 | NC_002331.1 | + | 42873 | 0.69 | 0.988924 |
|
Target: 5'- uGUCgcGCGCGUguGGUcaaacguuUGUGCGAAAu -3' miRNA: 3'- cCAGa-CGCGUAguCCA--------ACAUGCUUUu -5' |
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| 8735 | 5' | -48.8 | NC_002331.1 | + | 165088 | 0.7 | 0.981801 |
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Target: 5'- cGUCggGCGuCAUCAGGUUGUagcaucuuugACGGAc- -3' miRNA: 3'- cCAGa-CGC-GUAGUCCAACA----------UGCUUuu -5' |
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| 8735 | 5' | -48.8 | NC_002331.1 | + | 67324 | 1.09 | 0.014577 |
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Target: 5'- cGGUCUGCGCAUCAGGUUGUACGAAAAc -3' miRNA: 3'- -CCAGACGCGUAGUCCAACAUGCUUUU- -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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