miRNA: 3'- -GUC-AGUgUUGCGAgUUUGUAGAGAag -5'
miRNA: 3'- gucAGUGUUGCG---------AGUUUGUAGAGaAG- -5'
miRNA: 3'- gUCaGUGUUGCGAGU-----UUGUaGAGAAG- -5'
miRNA: 3'- -GUCAGUGUUGCGAGUUUGUAGAGAAG- -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 | |||||||
| 31532 | 3' | -46.4 | NC_006820.1 | + | 174763 | 0.68 | 0.999589 |
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Target: 5'- uCGGaUCA-AACGCUgGAACAUCUCUc- -3' miRNA: 3'- -GUC-AGUgUUGCGAgUUUGUAGAGAag -5' |
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| 31532 | 3' | -46.4 | NC_006820.1 | + | 14762 | 0.69 | 0.999357 |
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Target: 5'- --cUCACGACGCucugccucuUCAAACAUUUCaUCg -3' miRNA: 3'- gucAGUGUUGCG---------AGUUUGUAGAGaAG- -5' |
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| 31532 | 3' | -46.4 | NC_006820.1 | + | 16477 | 0.73 | 0.986668 |
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Target: 5'- uGG-CACGAUGCUCAcauguGACA-CUCUUCa -3' miRNA: 3'- gUCaGUGUUGCGAGU-----UUGUaGAGAAG- -5' |
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| 31532 | 3' | -46.4 | NC_006820.1 | + | 17616 | 1.12 | 0.019745 |
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Target: 5'- cCAGUCACAACGCUCAAACAUCUCUUCg -3' miRNA: 3'- -GUCAGUGUUGCGAGUUUGUAGAGAAG- -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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