miRNA: 3'- aGGUagCCUCGACCgACUUGaUUUuu -5'
miRNA: 3'- aGGUagCCUCGACCG-ACUUGAUuuuu -5'
miRNA: 3'- -AGGUaGCCUCG----ACCGACUUGa------UUUUU- -5'
miRNA: 3'- aggUAGCCUCGACCGa----CUUGaUUUUU- -5'
miRNA: 3'- -AGGUAGCCUCGACCGACUUGAUUUUU- -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 | |||||||
| 10415 | 3' | -49.5 | NC_002687.1 | + | 233251 | 0.66 | 0.999806 |
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Target: 5'- aCCAagGGGGCUGGaUGAACcAAGu- -3' miRNA: 3'- aGGUagCCUCGACCgACUUGaUUUuu -5' |
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| 10415 | 3' | -49.5 | NC_002687.1 | + | 2398 | 0.67 | 0.999516 |
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Target: 5'- cCCA--GGAGUUGGCgUGAACUGc--- -3' miRNA: 3'- aGGUagCCUCGACCG-ACUUGAUuuuu -5' |
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| 10415 | 3' | -49.5 | NC_002687.1 | + | 68296 | 0.69 | 0.997735 |
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Target: 5'- gUCCGaCGGAGCuucuUGGUUGAACgcgcaagGAAAGa -3' miRNA: 3'- -AGGUaGCCUCG----ACCGACUUGa------UUUUU- -5' |
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| 10415 | 3' | -49.5 | NC_002687.1 | + | 312717 | 0.69 | 0.996836 |
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Target: 5'- --aGUCGGGGCUGGUggucgGAACaAGAAGa -3' miRNA: 3'- aggUAGCCUCGACCGa----CUUGaUUUUU- -5' |
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| 10415 | 3' | -49.5 | NC_002687.1 | + | 295770 | 1.08 | 0.025861 |
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Target: 5'- gUCCAUCGGAGCUGGCUGAACUAAAAAa -3' miRNA: 3'- -AGGUAGCCUCGACCGACUUGAUUUUU- -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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