miRNA: 3'- agcgaaacAGAU------UGGUACGGGCACAG- -5'
miRNA: 3'- aGCGa-AACAGaUUGGU------------ACGGGCACAG- -5'
miRNA: 3'- -AGCGAAacagauUGGUACGGGCaCAG- -5'
miRNA: 3'- -AGCGAAaca---GAUUGGUACGGgCACAg -5'
miRNA: 3'- -AGCGAAACAGAUUGGUACGGGCACAG- -5'
Results 1 - 5 of 5 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 | |||||||
| 3511 | 3' | -50.9 | NC_001623.1 | + | 41636 | 0.66 | 0.99052 |
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Target: 5'- -------aUCUAaagaauGCCAUGCCCGUGUUu -3' miRNA: 3'- agcgaaacAGAU------UGGUACGGGCACAG- -5' |
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| 3511 | 3' | -50.9 | NC_001623.1 | + | 101440 | 0.67 | 0.979935 |
|
Target: 5'- aUGCaaUUGUCcGGCCGaugacggguuacUGCCCGUGUUu -3' miRNA: 3'- aGCGa-AACAGaUUGGU------------ACGGGCACAG- -5' |
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| 3511 | 3' | -50.9 | NC_001623.1 | + | 101788 | 0.67 | 0.969108 |
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Target: 5'- uUCGCUUgaaac-ACCAUGUCCGcGUCg -3' miRNA: 3'- -AGCGAAacagauUGGUACGGGCaCAG- -5' |
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| 3511 | 3' | -50.9 | NC_001623.1 | + | 47190 | 0.7 | 0.90064 |
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Target: 5'- gUCGCUUgaaacgCUGACCGUGUUgGUGUa -3' miRNA: 3'- -AGCGAAaca---GAUUGGUACGGgCACAg -5' |
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| 3511 | 3' | -50.9 | NC_001623.1 | + | 101654 | 1.12 | 0.004814 |
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Target: 5'- gUCGCUUUGUCUAACCAUGCCCGUGUCg -3' miRNA: 3'- -AGCGAAACAGAUUGGUACGGGCACAG- -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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