miRNA: 3'- -UUUUAUUAUCCGACUGGUGCACUGGG- -5'
miRNA: 3'- -UUUUAuUAUCCGACUGGUG-CaCUGgg -5'
miRNA: 3'- uuuuauuAUCCG--ACuGGUGCACUGGg -5'
miRNA: 3'- uuuuauuaUCCGACUGGU---------GCACU----GGG- -5'
miRNA: 3'- uUUUAUUAUC-C-GaCUgGUGCACUGGg -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 | |||||||
| 11172 | 3' | -47.6 | NC_002816.1 | + | 22606 | 1.1 | 0.011777 |
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Target: 5'- gAAAAUAAUAGGCUGACCACGUGACCCc -3' miRNA: 3'- -UUUUAUUAUCCGACUGGUGCACUGGG- -5' |
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| 11172 | 3' | -47.6 | NC_002816.1 | + | 61956 | 0.72 | 0.953067 |
|
Target: 5'- cAAGAUuGUAGGCUGACCACuGcGGCg- -3' miRNA: 3'- -UUUUAuUAUCCGACUGGUG-CaCUGgg -5' |
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| 11172 | 3' | -47.6 | NC_002816.1 | + | 16656 | 0.69 | 0.985929 |
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Target: 5'- ------uUGGGUgaUGuCCACGUGACCg -3' miRNA: 3'- uuuuauuAUCCG--ACuGGUGCACUGGg -5' |
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| 11172 | 3' | -47.6 | NC_002816.1 | + | 122128 | 0.68 | 0.995608 |
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Target: 5'- -------aAGGCUGGCCAcaacguuacCGUGAuuacCCCa -3' miRNA: 3'- uuuuauuaUCCGACUGGU---------GCACU----GGG- -5' |
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| 11172 | 3' | -47.6 | NC_002816.1 | + | 37623 | 0.66 | 0.998505 |
|
Target: 5'- cGAGUGGUAGaGaCcGAgCGCGUGGCCa -3' miRNA: 3'- uUUUAUUAUC-C-GaCUgGUGCACUGGg -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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