miRNA: 3'- ucgGCGAGUGGUCUCu--GCGGCUGCaa -5'
miRNA: 3'- ucGGCGAGUGGUCUCUG------CGGcUGCaa -5'
miRNA: 3'- uCGGCGAG-UGG-UCUCUGCgGCUGCaa -5'
miRNA: 3'- -UCGGCGAGUGGUCUCUGCGGCUGCAA- -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 | |||||||
| 22074 | 5' | -59.1 | NC_004927.1 | + | 57918 | 0.66 | 0.594213 |
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Target: 5'- --aCGCUCAUCGGAGuggUGCUGGCGa- -3' miRNA: 3'- ucgGCGAGUGGUCUCu--GCGGCUGCaa -5' |
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| 22074 | 5' | -59.1 | NC_004927.1 | + | 20238 | 0.67 | 0.501437 |
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Target: 5'- -uCCGCUCGCCGGGGACggacuuGCC-ACGg- -3' miRNA: 3'- ucGGCGAGUGGUCUCUG------CGGcUGCaa -5' |
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| 22074 | 5' | -59.1 | NC_004927.1 | + | 71187 | 0.79 | 0.091035 |
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Target: 5'- cGCCGCUCuACCaAGAGACGgCGACGa- -3' miRNA: 3'- uCGGCGAG-UGG-UCUCUGCgGCUGCaa -5' |
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| 22074 | 5' | -59.1 | NC_004927.1 | + | 42712 | 1.05 | 0.001068 |
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Target: 5'- uAGCCGCUCACCAGAGACGCCGACGUUg -3' miRNA: 3'- -UCGGCGAGUGGUCUCUGCGGCUGCAA- -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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