miRNA: 3'- -CGUCGGCGCUAUGGAAUUGGUCUGUU- -5'
miRNA: 3'- -CGUCGGC------GCUA------------UGGA---AUUGGUCUGUU- -5'
miRNA: 3'- cGUCGGCG--CUAUGGaaUUGG-UCUGUu -5'
miRNA: 3'- -CGUCGGCGCUA----UGGaAUUGgUC-UGUU- -5'
miRNA: 3'- -CGuCGGCGcUAUGgaaUUGGUCUGUU- -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
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R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 17016 | 5' | -51.4 | NC_004333.2 | + | 39322 | 1.09 | 0.001695 |
|
Target: 5'- cGCAGCCGCGAUACCUUAACCAGACAAg -3' miRNA: 3'- -CGUCGGCGCUAUGGAAUUGGUCUGUU- -5' |
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| 17016 | 5' | -51.4 | NC_004333.2 | + | 40235 | 0.67 | 0.802998 |
|
Target: 5'- cGCGGCCGgccaacCGAUcgacgaauucgaACCUuucUGACUAGGCAAa -3' miRNA: 3'- -CGUCGGC------GCUA------------UGGA---AUUGGUCUGUU- -5' |
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| 17016 | 5' | -51.4 | NC_004333.2 | + | 42291 | 0.66 | 0.841594 |
|
Target: 5'- cCGGCCGCaaGGUGCC--GACCgAGGCGu -3' miRNA: 3'- cGUCGGCG--CUAUGGaaUUGG-UCUGUu -5' |
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| 17016 | 5' | -51.4 | NC_004333.2 | + | 45434 | 0.71 | 0.590623 |
|
Target: 5'- gGCGGCCGCGAUcucgGCUgUGACgGGcACGAa -3' miRNA: 3'- -CGUCGGCGCUA----UGGaAUUGgUC-UGUU- -5' |
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| 17016 | 5' | -51.4 | NC_004333.2 | + | 45766 | 0.69 | 0.671544 |
|
Target: 5'- cGCuGCCGCuGUACggcGACCAGGCGAc -3' miRNA: 3'- -CGuCGGCGcUAUGgaaUUGGUCUGUU- -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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