miRNA: 3'- aGGcCCACAUGAgGG--UCGCUgUACUc -5'
miRNA: 3'- -AGGC-CCACAUGaGGGUCGCUguacuc -5'
miRNA: 3'- aGGCCCaCa--UgAGGGUCGC-UGUACUc -5'
miRNA: 3'- aGGCCCa--CAUG-----AGGGU-CGCUGUaCUC- -5'
miRNA: 3'- -AGGCCCACAUGAGGGUCGCUGUACUC- -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 | |||||||
| 27439 | 5' | -55.9 | NC_005869.1 | + | 2821 | 0.66 | 0.558754 |
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Target: 5'- aCCuGGUGUGCUgCCagAGCGGgAUGGu -3' miRNA: 3'- aGGcCCACAUGAgGG--UCGCUgUACUc -5' |
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| 27439 | 5' | -55.9 | NC_005869.1 | + | 9042 | 0.66 | 0.525713 |
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Target: 5'- gUCCGaGGUGUGCaUCCAGCGGg----- -3' miRNA: 3'- -AGGC-CCACAUGaGGGUCGCUguacuc -5' |
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| 27439 | 5' | -55.9 | NC_005869.1 | + | 8239 | 0.67 | 0.504099 |
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Target: 5'- cUCGGGcGgggGgUCCCAGCGcACGUGGu -3' miRNA: 3'- aGGCCCaCa--UgAGGGUCGC-UGUACUc -5' |
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| 27439 | 5' | -55.9 | NC_005869.1 | + | 19152 | 0.7 | 0.331608 |
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Target: 5'- cCCGGGcugGUGCaguucUCCCAgGCGACG-GAGa -3' miRNA: 3'- aGGCCCa--CAUG-----AGGGU-CGCUGUaCUC- -5' |
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| 27439 | 5' | -55.9 | NC_005869.1 | + | 1591 | 1.08 | 0.000536 |
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Target: 5'- gUCCGGGUGUACUCCCAGCGACAUGAGc -3' miRNA: 3'- -AGGCCCACAUGAGGGUCGCUGUACUC- -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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