miRNA: 3'- -CCGCUCGGu--GUGuuuGUUAGGUUUGa -5'
miRNA: 3'- -CCGc------UCGGUGUg-------UUUGUUAGGUUUga -5'
miRNA: 3'- ccGCUCGGUGUGUUUGuuAGG-UUUGa -5'
miRNA: 3'- -CCGc---UCGGUGU--------GUUUGUuaGGUUUGa -5'
miRNA: 3'- -CCGCUCGGUGUGUUUGUUAGGUUUGA- -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 | |||||||
| 13646 | 5' | -47.8 | NC_003491.1 | + | 2057 | 0.66 | 0.438727 |
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Target: 5'- uGGUGAGCUucgUGCcc-CAAUCCGAGCa -3' miRNA: 3'- -CCGCUCGGu--GUGuuuGUUAGGUUUGa -5' |
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| 13646 | 5' | -47.8 | NC_003491.1 | + | 5208 | 0.66 | 0.426601 |
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Target: 5'- uGGCuugccaaAGCCACAaccggucaGAACGAUCCGAAa- -3' miRNA: 3'- -CCGc------UCGGUGUg-------UUUGUUAGGUUUga -5' |
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| 13646 | 5' | -47.8 | NC_003491.1 | + | 2522 | 0.66 | 0.414676 |
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Target: 5'- -uUGGGUCACACAGACcuUCCuGAACc -3' miRNA: 3'- ccGCUCGGUGUGUUUGuuAGG-UUUGa -5' |
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| 13646 | 5' | -47.8 | NC_003491.1 | + | 2133 | 0.68 | 0.327063 |
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Target: 5'- cGGCuacaAGCCGCAagauggcuCGAACGcgCCGAGCa -3' miRNA: 3'- -CCGc---UCGGUGU--------GUUUGUuaGGUUUGa -5' |
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| 13646 | 5' | -47.8 | NC_003491.1 | + | 2534 | 1.11 | 0.000174 |
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Target: 5'- aGGCGAGCCACACAAACAAUCCAAACUu -3' miRNA: 3'- -CCGCUCGGUGUGUUUGUUAGGUUUGA- -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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