miRNA: 3'- cAGAGauGCUGgG---------CCCGUGGACGGAG- -5'
miRNA: 3'- cagagaUGCUGGGCCCGUGGa-------CGGAG- -5'
miRNA: 3'- -CAGa---GAUgCUGGgcCCGUGGACGGAG- -5'
miRNA: 3'- -CAGAGAUGCUGGGCCCGUGGACGGAG- -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 | |||||||
| 767 | 5' | -59.7 | NC_000852.3 | + | 2720 | 0.67 | 0.870586 |
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Target: 5'- aUCUC--CGACgUugucaaaggGGGCACCUGCUUCa -3' miRNA: 3'- cAGAGauGCUGgG---------CCCGUGGACGGAG- -5' |
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| 767 | 5' | -59.7 | NC_000852.3 | + | 52611 | 0.67 | 0.849147 |
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Target: 5'- -----aGCGACCCGGGUGCCaacggaagGCUUCu -3' miRNA: 3'- cagagaUGCUGGGCCCGUGGa-------CGGAG- -5' |
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| 767 | 5' | -59.7 | NC_000852.3 | + | 3012 | 0.67 | 0.84165 |
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Target: 5'- cGUCgaugUUAaGACC--GGCACCUGCCUCu -3' miRNA: 3'- -CAGa---GAUgCUGGgcCCGUGGACGGAG- -5' |
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| 767 | 5' | -59.7 | NC_000852.3 | + | 301671 | 1.09 | 0.002857 |
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Target: 5'- gGUCUCUACGACCCGGGCACCUGCCUCg -3' miRNA: 3'- -CAGAGAUGCUGGGCCCGUGGACGGAG- -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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