miRNA: 3'- -CCUAGaCAGa-----GGCC-----ACCUA-CACAGCC- -5'
miRNA: 3'- -CCUAGA---------------CaGAGGccACCUACACAGCC- -5'
miRNA: 3'- -CCUAga-----CaGAGGCCACCua--CACAGCC- -5'
miRNA: 3'- -CCUAGACAGAGGCCACCUACACAGCC- -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 | |||||||
| 1513 | 5' | -53 | NC_001335.1 | + | 2820 | 0.68 | 0.772885 |
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Target: 5'- gGGAUC-GUCaccagaCCGGgcaucUGGAUcGUGUCGGu -3' miRNA: 3'- -CCUAGaCAGa-----GGCC-----ACCUA-CACAGCC- -5' |
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| 1513 | 5' | -53 | NC_001335.1 | + | 41696 | 0.7 | 0.616046 |
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Target: 5'- aGGAUCUugccaucgucacggaGcCUCCacUGGGUGUGUCGGu -3' miRNA: 3'- -CCUAGA---------------CaGAGGccACCUACACAGCC- -5' |
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| 1513 | 5' | -53 | NC_001335.1 | + | 13834 | 0.72 | 0.535566 |
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Target: 5'- aGGAUguaagugGcCUCCGGUGGuuucGUGUCGGu -3' miRNA: 3'- -CCUAga-----CaGAGGCCACCua--CACAGCC- -5' |
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| 1513 | 5' | -53 | NC_001335.1 | + | 41633 | 1.14 | 0.000963 |
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Target: 5'- uGGAUCUGUCUCCGGUGGAUGUGUCGGg -3' miRNA: 3'- -CCUAGACAGAGGCCACCUACACAGCC- -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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