miRNA: 3'- -GGGGUCUAUGGUCGCCCUACACCUGC- -5'
miRNA: 3'- gGGGUCUAUGGU-----------CGCCCUacACCUGC- -5'
miRNA: 3'- gGGGUCUAUGg------UCG-CCCUa--CACCU-GC- -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 | |||||||
| 1073 | 3' | -56.1 | NC_000929.1 | + | 31110 | 1.11 | 0.00037 |
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Target: 5'- cCCCCAGAUACCAGCGGGAUGUGGACGg -3' miRNA: 3'- -GGGGUCUAUGGUCGCCCUACACCUGC- -5' |
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| 1073 | 3' | -56.1 | NC_000929.1 | + | 22313 | 0.72 | 0.261404 |
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Target: 5'- aCCCGGAUAUCAgcgcaaguaucGCGGGAa-UGGGCGa -3' miRNA: 3'- gGGGUCUAUGGU-----------CGCCCUacACCUGC- -5' |
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| 1073 | 3' | -56.1 | NC_000929.1 | + | 17523 | 0.68 | 0.466253 |
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Target: 5'- aCCCGGAUACagggaaaGGCuGGGAagcGUGGAgCGa -3' miRNA: 3'- gGGGUCUAUGg------UCG-CCCUa--CACCU-GC- -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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