miRNA: 3'- -CCGAGUUGCGGAAGCCUCGGCGCGCG- -5'
miRNA: 3'- -CCga-GUUGCGGAag-----CCUCGGCGCGCG- -5'
miRNA: 3'- -CCGa-GUU-----GCGGaaGCC---UCGGCGCGCG- -5'
miRNA: 3'- ccgaguUGCGGAAGCcuCGGCGCGCG- -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 | |||||||
| 8396 | 5' | -58.7 | NC_002076.2 | + | 3161 | 1.13 | 0.000003 |
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Target: 5'- gGGCUCAACGCCUUCGGAGCCGCGCGCu -3' miRNA: 3'- -CCGAGUUGCGGAAGCCUCGGCGCGCG- -5' |
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| 8396 | 5' | -58.7 | NC_002076.2 | + | 3790 | 0.78 | 0.004533 |
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Target: 5'- gGGaggCAAUGCCUccccccgGGGGCCGCGCGCg -3' miRNA: 3'- -CCga-GUUGCGGAag-----CCUCGGCGCGCG- -5' |
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| 8396 | 5' | -58.7 | NC_002076.2 | + | 3716 | 0.7 | 0.025007 |
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Target: 5'- aGGCgcCAAaaaacCGUCggCGGgggGGCCGCGCGCu -3' miRNA: 3'- -CCGa-GUU-----GCGGaaGCC---UCGGCGCGCG- -5' |
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| 8396 | 5' | -58.7 | NC_002076.2 | + | 3188 | 0.68 | 0.03685 |
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Target: 5'- -----uACGCCUUCG--GCUGCGCGCg -3' miRNA: 3'- ccgaguUGCGGAAGCcuCGGCGCGCG- -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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