miRNA: 3'- uuuCUGGAGCUCgCga----AGCUGAUGGg -5'
miRNA: 3'- -UUUCUGG-AGCuCGCGA------AGCUGaUGGG- -5'
miRNA: 3'- uUUCugGAG--CUCGCGaa--GC-----UGAUGGG- -5'
miRNA: 3'- -UUUCUGGAGCUCGCGAAGCUGAUGGG- -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 | |||||||
| 1316 | 3' | -53.1 | NC_001331.1 | + | 5249 | 0.66 | 0.247649 |
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Target: 5'- --uGGCCUCGGGgGaggucaUUGGCUGCCg -3' miRNA: 3'- uuuCUGGAGCUCgCga----AGCUGAUGGg -5' |
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| 1316 | 3' | -53.1 | NC_001331.1 | + | 984 | 0.67 | 0.20539 |
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Target: 5'- uGAAGGCCaUUG-GCGCUacaucgUCGGC-GCCCu -3' miRNA: 3'- -UUUCUGG-AGCuCGCGA------AGCUGaUGGG- -5' |
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| 1316 | 3' | -53.1 | NC_001331.1 | + | 7038 | 0.69 | 0.139358 |
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Target: 5'- cGAGugCUCggGAGCGCggggCGgagaaGCUGCCCc -3' miRNA: 3'- uUUCugGAG--CUCGCGaa--GC-----UGAUGGG- -5' |
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| 1316 | 3' | -53.1 | NC_001331.1 | + | 3196 | 1.09 | 8.6e-05 |
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Target: 5'- aAAAGACCUCGAGCGCUUCGACUACCCc -3' miRNA: 3'- -UUUCUGGAGCUCGCGAAGCUGAUGGG- -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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