miRNA: 3'- gaguCCCUUGAGC-CUCUGC---AGACgCa -5'
miRNA: 3'- -GAGUCCCUUGa-GCCuCugCAGA----CGca -5'
miRNA: 3'- gagUCCCUUGA--------GCCUCUGCAGA----------CGCA- -5'
miRNA: 3'- -GAGUCCCUUGAGCCUCUGCAGACGCA- -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 | |||||||
| 6314 | 5' | -55.6 | NC_001844.1 | + | 116249 | 0.66 | 0.899369 |
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Target: 5'- ---cGGGGACUCGcGGGACGggcUCUGgGa -3' miRNA: 3'- gaguCCCUUGAGC-CUCUGC---AGACgCa -5' |
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| 6314 | 5' | -55.6 | NC_001844.1 | + | 143597 | 0.67 | 0.879019 |
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Target: 5'- cCUCGGGGAACagCGG-GugGUCUaucaGCu- -3' miRNA: 3'- -GAGUCCCUUGa-GCCuCugCAGA----CGca -5' |
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| 6314 | 5' | -55.6 | NC_001844.1 | + | 133170 | 0.69 | 0.788702 |
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Target: 5'- --uGGGGAACUaguaugggUGGAGGCGUCUugacauguacGCGUg -3' miRNA: 3'- gagUCCCUUGA--------GCCUCUGCAGA----------CGCA- -5' |
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| 6314 | 5' | -55.6 | NC_001844.1 | + | 115593 | 1.08 | 0.003772 |
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Target: 5'- gCUCAGGGAACUCGGAGACGUCUGCGUa -3' miRNA: 3'- -GAGUCCCUUGAGCCUCUGCAGACGCA- -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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