miRNA: 3'- aCCCG--------AGCUGGGUUuuuauCCCGCUc -5'
miRNA: 3'- accCGAGCUGGGuuuUUAUC-CCGCUC- -5'
miRNA: 3'- aCCCG----AGCU-GGGUUUUuaUCC-CGCUC- -5'
miRNA: 3'- -ACCCGAGCUGGGUUUUUAUCCCGCUC- -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 | |||||||
| 7592 | 5' | -53.2 | NC_001963.1 | + | 2590 | 0.66 | 0.165176 |
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Target: 5'- aGGGCcgaacaauUCGGCCCGGu----GGGUGAc -3' miRNA: 3'- aCCCG--------AGCUGGGUUuuuauCCCGCUc -5' |
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| 7592 | 5' | -53.2 | NC_001963.1 | + | 3769 | 0.71 | 0.062679 |
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Target: 5'- --uGCUCGACCCu--GGUGGuGGCGGGc -3' miRNA: 3'- accCGAGCUGGGuuuUUAUC-CCGCUC- -5' |
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| 7592 | 5' | -53.2 | NC_001963.1 | + | 3554 | 0.73 | 0.050631 |
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Target: 5'- cGGGCagugUCGAuCCCGAGA--AGGcGCGAGg -3' miRNA: 3'- aCCCG----AGCU-GGGUUUUuaUCC-CGCUC- -5' |
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| 7592 | 5' | -53.2 | NC_001963.1 | + | 1557 | 1.1 | 3.8e-05 |
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Target: 5'- gUGGGCUCGACCCAAAAAUAGGGCGAGa -3' miRNA: 3'- -ACCCGAGCUGGGUUUUUAUCCCGCUC- -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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