miRNA: 3'- -CGCGUG-------CCAUGAGgGGCC---UGAGGuag -5'
miRNA: 3'- -CGCG--UgCCAUGa-GGGGCcUGAGGUAG- -5'
miRNA: 3'- -CGCGUGCCAUGAGGGGCCUGAGGUAG- -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 | |||||||
| 1230 | 5' | -57.8 | NC_001271.1 | + | 36508 | 0.67 | 0.444657 |
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Target: 5'- aGCGCACucccuugGGUACUCgCCGGgacACUCUu-- -3' miRNA: 3'- -CGCGUG-------CCAUGAGgGGCC---UGAGGuag -5' |
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| 1230 | 5' | -57.8 | NC_001271.1 | + | 32501 | 0.71 | 0.230938 |
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Target: 5'- gGCGCuuGgGGUACagCCCUGcGCUCCGUCa -3' miRNA: 3'- -CGCG--UgCCAUGa-GGGGCcUGAGGUAG- -5' |
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| 1230 | 5' | -57.8 | NC_001271.1 | + | 18150 | 1.12 | 0.000243 |
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Target: 5'- aGCGCACGGUACUCCCCGGACUCCAUCa -3' miRNA: 3'- -CGCGUGCCAUGAGGGGCCUGAGGUAG- -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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