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miRNA: 3'- -GCUGGCUUUGCCAGAACCCAGCCCGC- -5'
miRNA: 3'- gCUGGCUU-UGCCa-GAACCCa--------GCCCGC- -5'
miRNA: 3'- gCUGGCUUUG------------CCAGAAcCCAGC-CCGc -5'
miRNA: 3'- gCUGGCUUuGCCaGaacCCA-GCCCGC- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 1298 | 5' | -56.3 | NC_001331.1 | + | 274 | 1.1 | 0.000043 |
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Target: 5'- cCGACCGAAACGGUCUUGGGUCGGGCGg -3' miRNA: 3'- -GCUGGCUUUGCCAGAACCCAGCCCGC- -5' |
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| 1298 | 5' | -56.3 | NC_001331.1 | + | 388 | 0.76 | 0.030739 |
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Target: 5'- gGGCCGGAcGCGGggCUUGGGccuggcuugCGGGCGg -3' miRNA: 3'- gCUGGCUU-UGCCa-GAACCCa--------GCCCGC- -5' |
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| 1298 | 5' | -56.3 | NC_001331.1 | + | 107 | 0.68 | 0.118746 |
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Target: 5'- gGACCGAGGCguagauuuccccGGUCUU-GGUCGaGGUa -3' miRNA: 3'- gCUGGCUUUG------------CCAGAAcCCAGC-CCGc -5' |
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| 1298 | 5' | -56.3 | NC_001331.1 | + | 6890 | 0.67 | 0.153011 |
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Target: 5'- uGACCGGAuCGGcCac-GGUgCGGGCGg -3' miRNA: 3'- gCUGGCUUuGCCaGaacCCA-GCCCGC- -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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