miRNA: 3'- -GCGCAGCG---------CAUgGGAAUC-GCU--------AGUUG- -5'
miRNA: 3'- -GCGCAGCGCaUGGGAAu----CG----CUAGUUG- -5'
miRNA: 3'- gCGCAGCG-CAUGGGa----AUCGCUAGuug -5'
miRNA: 3'- -GCGCAGCGCAUGGGAAUCGCUAGUUG- -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 | |||||||
| 16670 | 3' | -52.5 | NC_004156.1 | + | 174774 | 0.66 | 0.994743 |
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Target: 5'- aCGUGUCGCuuugaaaauGUAgCCUUGGaCGAguugaccaUCAGCu -3' miRNA: 3'- -GCGCAGCG---------CAUgGGAAUC-GCU--------AGUUG- -5' |
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| 16670 | 3' | -52.5 | NC_004156.1 | + | 69745 | 0.67 | 0.989647 |
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Target: 5'- aCGUGUCGCGgAUCCUUcaaacGCuucuGGUCAACu -3' miRNA: 3'- -GCGCAGCGCaUGGGAAu----CG----CUAGUUG- -5' |
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| 16670 | 3' | -52.5 | NC_004156.1 | + | 130572 | 0.7 | 0.94694 |
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Target: 5'- uGCGUCGCuGUAUCCguaccUGGUGGUCu-- -3' miRNA: 3'- gCGCAGCG-CAUGGGa----AUCGCUAGuug -5' |
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| 16670 | 3' | -52.5 | NC_004156.1 | + | 63717 | 1.11 | 0.007871 |
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Target: 5'- aCGCGUCGCGUACCCUUAGCGAUCAACu -3' miRNA: 3'- -GCGCAGCGCAUGGGAAUCGCUAGUUG- -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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