miRNA: 3'- aCCu---CGGGGCUuuGGGUu-UCGGUuGG- -5'
miRNA: 3'- aCCUCGGGGCU--UUGGGuuuCGGUUGg -5'
miRNA: 3'- aCC-UCGGGGCuuUGgGUUUCGGUUgg -5'
miRNA: 3'- -ACCUCGGG-GCuuUGGGUuUC---------GGUUGG- -5'
miRNA: 3'- -ACCUCGGGGCUUUGGGUUUCGGUUGG- -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 | |||||||
| 29664 | 3' | -54.4 | NC_006260.1 | + | 1048 | 0.66 | 0.126075 |
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Target: 5'- aGGugauGCCCCGG--UCCAccAGCCAcCCg -3' miRNA: 3'- aCCu---CGGGGCUuuGGGUu-UCGGUuGG- -5' |
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| 29664 | 3' | -54.4 | NC_006260.1 | + | 1895 | 0.71 | 0.050814 |
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Target: 5'- aGGAGCUCCGGugGACUUu--GCCGACa -3' miRNA: 3'- aCCUCGGGGCU--UUGGGuuuCGGUUGg -5' |
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| 29664 | 3' | -54.4 | NC_006260.1 | + | 3313 | 0.72 | 0.038192 |
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Target: 5'- aGGcAGCCCUGguGCgCAGAGCCGAg- -3' miRNA: 3'- aCC-UCGGGGCuuUGgGUUUCGGUUgg -5' |
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| 29664 | 3' | -54.4 | NC_006260.1 | + | 1185 | 0.73 | 0.03555 |
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Target: 5'- gUGGGGCCCuCGcuGCCCGcGGacauuaaaaCCAACCg -3' miRNA: 3'- -ACCUCGGG-GCuuUGGGUuUC---------GGUUGG- -5' |
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| 29664 | 3' | -54.4 | NC_006260.1 | + | 2299 | 1.13 | 1.3e-05 |
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Target: 5'- cUGGAGCCCCGAAACCCAAAGCCAACCa -3' miRNA: 3'- -ACCUCGGGGCUUUGGGUUUCGGUUGG- -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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