miRNA: 3'- -UCGGG--------CUGcUGGUGGGG-----UCCG----------UGCAG- -5'
miRNA: 3'- -UCGGGC--UGCUGG-UGGGG--------------UCCguGCAG- -5'
miRNA: 3'- -UCGGGCUGCUGGUGGGGUCCGUGCAG- -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 | |||||||
| 2301 | 5' | -61.9 | NC_001408.1 | + | 3894 | 0.66 | 0.06374 |
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Target: 5'- gGGCCCucccuccaGACuACCACCCCuuuauGGGUgcuugaggagGCGUCg -3' miRNA: 3'- -UCGGG--------CUGcUGGUGGGG-----UCCG----------UGCAG- -5' |
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| 2301 | 5' | -61.9 | NC_001408.1 | + | 264 | 0.71 | 0.023631 |
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Target: 5'- gGGCCCGgaGCGACUgACCCCugccgagaacucagAGGguCGUCg -3' miRNA: 3'- -UCGGGC--UGCUGG-UGGGG--------------UCCguGCAG- -5' |
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| 2301 | 5' | -61.9 | NC_001408.1 | + | 322 | 1.08 | 1e-05 |
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Target: 5'- gAGCCCGACGACCACCCCAGGCACGUCu -3' miRNA: 3'- -UCGGGCUGCUGGUGGGGUCCGUGCAG- -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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