miRNA: 3'- -GCUG--AugGCCGUgUUUGUCCUGa--UGU- -5'
miRNA: 3'- gCuGAugGCCGU-----------GUuUGUCCUGAUGu -5'
miRNA: 3'- gCUGA-------------UGGCCgUGUUUGUCCUGaUGU- -5'
miRNA: 3'- -GCUGAUG--GCCGUGUUUGucCUGAUgu -5'
miRNA: 3'- -GCUGAUGGCCGUGUUUGUCCUGAUGU- -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 | |||||||
| 31999 | 5' | -51 | NC_006949.1 | + | 33822 | 0.66 | 0.889301 |
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Target: 5'- aCGAUguUugCGGCA-AAGCAGGAUggcGCAa -3' miRNA: 3'- -GCUG--AugGCCGUgUUUGUCCUGa--UGU- -5' |
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| 31999 | 5' | -51 | NC_006949.1 | + | 28592 | 0.66 | 0.881557 |
|
Target: 5'- aGcCUugCGGCGuuccuguagcuCAcACAGGGCUGCu -3' miRNA: 3'- gCuGAugGCCGU-----------GUuUGUCCUGAUGu -5' |
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| 31999 | 5' | -51 | NC_006949.1 | + | 4165 | 0.67 | 0.846971 |
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Target: 5'- aGGCUggcauagagaagcGCCGG-GCGAACAGGAUaGCGc -3' miRNA: 3'- gCUGA-------------UGGCCgUGUUUGUCCUGaUGU- -5' |
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| 31999 | 5' | -51 | NC_006949.1 | + | 44557 | 0.68 | 0.769389 |
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Target: 5'- uCGGCUACauCGGCACAGACucGAUUGg- -3' miRNA: 3'- -GCUGAUG--GCCGUGUUUGucCUGAUgu -5' |
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| 31999 | 5' | -51 | NC_006949.1 | + | 19881 | 1.1 | 0.00209 |
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Target: 5'- uCGACUACCGGCACAAACAGGACUACAg -3' miRNA: 3'- -GCUGAUGGCCGUGUUUGUCCUGAUGU- -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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