miRNA: 3'- gaCCUCAGCCAGAg------------GCUCCagUGAAG- -5'
miRNA: 3'- gACCUCAGCCAGaGGCU---CC-AGuGa---AG- -5'
miRNA: 3'- -GACCUCa------------GCCAGaGGCUCCaGUGaag -5'
Results 1 - 3 of 3 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 | |||||||
| 31259 | 5' | -55.2 | NC_006560.1 | + | 8863 | 0.66 | 0.932662 |
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Target: 5'- -cGGGGUCGGUCUggggugggggaggCGGGGg-GCUUCg -3' miRNA: 3'- gaCCUCAGCCAGAg------------GCUCCagUGAAG- -5' |
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| 31259 | 5' | -55.2 | NC_006560.1 | + | 15836 | 0.66 | 0.91868 |
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Target: 5'- gUGGAGUCGGUCgCCGAccaGGaUCuCguagUCg -3' miRNA: 3'- gACCUCAGCCAGaGGCU---CC-AGuGa---AG- -5' |
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| 31259 | 5' | -55.2 | NC_006560.1 | + | 75204 | 0.67 | 0.89135 |
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Target: 5'- gCUGGAGgccgccgcgcgcgCGGUCgCCGAGG-CGCg-- -3' miRNA: 3'- -GACCUCa------------GCCAGaGGCUCCaGUGaag -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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