miRNA: 3'- -GCGA----GC---------------UCGCCAGGUGAGACCgcCGG- -5'
miRNA: 3'- -GCGAGCUCGCCAGGugaGAC-CGCCGG- -5'
miRNA: 3'- gCGAGCU-CGCCAGGugAgaCCGCCGG- -5'
miRNA: 3'- -GCGAGCUCGCCAGGUGAGACCGCCGG- -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 | |||||||
| 30391 | 5' | -60.9 | NC_006458.1 | + | 161 | 0.72 | 0.000958 |
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Target: 5'- cCGCUcgagCGuaaugaagaccuauaAGCGGUCCGCUCUGGa-GCCu -3' miRNA: 3'- -GCGA----GC---------------UCGCCAGGUGAGACCgcCGG- -5' |
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| 30391 | 5' | -60.9 | NC_006458.1 | + | 349 | 0.72 | 0.000868 |
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Target: 5'- uCGUUCGAGUGGUUC---CUGcGCGGCCc -3' miRNA: 3'- -GCGAGCUCGCCAGGugaGAC-CGCCGG- -5' |
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| 30391 | 5' | -60.9 | NC_006458.1 | + | 247 | 0.73 | 0.000707 |
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Target: 5'- uGCUUGGuGUGGUCCugUg-GGUGGCCc -3' miRNA: 3'- gCGAGCU-CGCCAGGugAgaCCGCCGG- -5' |
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| 30391 | 5' | -60.9 | NC_006458.1 | + | 172 | 1.11 | 0 |
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Target: 5'- aCGCUCGAGCGGUCCACUCUGGCGGCCu -3' miRNA: 3'- -GCGAGCUCGCCAGGUGAGACCGCCGG- -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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