miRNA: 3'- -GCCGCCAGu-UAcCCGUC--UUGA-CCUag -5'
miRNA: 3'- gCCGCCAgUUACC-CGuCUUG----ACCUag -5'
miRNA: 3'- -GCCGcc--AGUuaCC-CGUCUUGACCUag -5'
miRNA: 3'- -GCCGCCAGUUACCCGUCUUGACCUAG- -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 | |||||||
| 30701 | 3' | -54.6 | NC_006552.1 | + | 44963 | 0.67 | 0.748484 |
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Target: 5'- aCGGCGGUCuuGUaGGCAGucAGCUuGGAg- -3' miRNA: 3'- -GCCGCCAGu-UAcCCGUC--UUGA-CCUag -5' |
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| 30701 | 3' | -54.6 | NC_006552.1 | + | 24240 | 0.67 | 0.695396 |
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Target: 5'- aGGCGGUgGAUGGuGCcGGACcgcaUGGAc- -3' miRNA: 3'- gCCGCCAgUUACC-CGuCUUG----ACCUag -5' |
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| 30701 | 3' | -54.6 | NC_006552.1 | + | 52762 | 0.68 | 0.684551 |
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Target: 5'- uCGGCcgccUCGcgGGuGCGGAACUGGAa- -3' miRNA: 3'- -GCCGcc--AGUuaCC-CGUCUUGACCUag -5' |
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| 30701 | 3' | -54.6 | NC_006552.1 | + | 6087 | 1.11 | 0.00103 |
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Target: 5'- cCGGCGGUCAAUGGGCAGAACUGGAUCa -3' miRNA: 3'- -GCCGCCAGUUACCCGUCUUGACCUAG- -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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