miRNA: 3'- -GCGUCACCGa-------------CAGuaCuGUCUCUGCa -5'
miRNA: 3'- gCGUCaCCGa-------------CaGuaCUGUCUCUGCA- -5'
miRNA: 3'- gCG-UCACCGACAGua----CUGUCUCUGca -5'
miRNA: 3'- -GCGUCACCGACAGUACUGUCUCUGCA- -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 | |||||||
| 28370 | 5' | -53.8 | NC_005946.1 | + | 88274 | 0.66 | 0.911434 |
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Target: 5'- aCGCGGUGGUcaagguggcaaaggGUCccGcCGGAGACGg -3' miRNA: 3'- -GCGUCACCGa-------------CAGuaCuGUCUCUGCa -5' |
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| 28370 | 5' | -53.8 | NC_005946.1 | + | 76357 | 0.67 | 0.891566 |
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Target: 5'- aGCGG-GGCgccuggaucucaggGcCcgGACGGAGACGUg -3' miRNA: 3'- gCGUCaCCGa-------------CaGuaCUGUCUCUGCA- -5' |
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| 28370 | 5' | -53.8 | NC_005946.1 | + | 13151 | 0.72 | 0.632821 |
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Target: 5'- gGCuGGUGGCUGUUcccaggGGCAGGGACa- -3' miRNA: 3'- gCG-UCACCGACAGua----CUGUCUCUGca -5' |
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| 28370 | 5' | -53.8 | NC_005946.1 | + | 31378 | 1.08 | 0.003263 |
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Target: 5'- gCGCAGUGGCUGUCAUGACAGAGACGUa -3' miRNA: 3'- -GCGUCACCGACAGUACUGUCUCUGCA- -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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