miRNA: 3'- gGUagUGGCuuuAGCCACGCCCGCUu -5'
miRNA: 3'- -GGuaGUGGCUuuAGCCAC-GCCCGcuu -5'
miRNA: 3'- gguagUGGCUUUAGCCACg-----CCCGCUu -5'
miRNA: 3'- -GGUAGUGGCUUUAGCCACGCCCGCUU- -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 | |||||||
| 3509 | 5' | -54.4 | NC_001623.1 | + | 84584 | 0.69 | 0.81068 |
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Target: 5'- aCA--AUCGu--UCGGUGCGGGCGGg -3' miRNA: 3'- gGUagUGGCuuuAGCCACGCCCGCUu -5' |
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| 3509 | 5' | -54.4 | NC_001623.1 | + | 95499 | 0.72 | 0.683984 |
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Target: 5'- gCCcgCACCGAuuUCGGUGaUGGGUa-- -3' miRNA: 3'- -GGuaGUGGCUuuAGCCAC-GCCCGcuu -5' |
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| 3509 | 5' | -54.4 | NC_001623.1 | + | 33176 | 0.73 | 0.611288 |
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Target: 5'- ----uGCCGAGAUCGGUGguacaaGGGCGAu -3' miRNA: 3'- gguagUGGCUUUAGCCACg-----CCCGCUu -5' |
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| 3509 | 5' | -54.4 | NC_001623.1 | + | 95655 | 1.08 | 0.004001 |
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Target: 5'- cCCAUCACCGAAAUCGGUGCGGGCGAAa -3' miRNA: 3'- -GGUAGUGGCUUUAGCCACGCCCGCUU- -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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