miRNA: 3'- -ACUUGa------AG-CACuuCGGUACCCG--CGau -5'
miRNA: 3'- aCUUGaa-----GCa--CUUCGGUaCCCGCGau -5'
miRNA: 3'- aCUUGaaGC-------------ACUUCGGUA---CCCGCGau -5'
miRNA: 3'- -ACUUGAAGCACUUCGGUACCCGCGAU- -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 | |||||||
| 18411 | 3' | -53.1 | NC_004681.1 | + | 24064 | 0.66 | 0.840304 |
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Target: 5'- cUGGACgccauugUCgGUGgcGCCGUGGGCcaGCa- -3' miRNA: 3'- -ACUUGa------AG-CACuuCGGUACCCG--CGau -5' |
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| 18411 | 3' | -53.1 | NC_004681.1 | + | 69232 | 0.67 | 0.81275 |
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Target: 5'- cGAGCcgguaggCGaggGAGGCCA-GGGCGCg- -3' miRNA: 3'- aCUUGaa-----GCa--CUUCGGUaCCCGCGau -5' |
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| 18411 | 3' | -53.1 | NC_004681.1 | + | 48767 | 0.67 | 0.792407 |
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Target: 5'- aGGACggCGgcuacaccuggagUGAGGCCGUcgaGGGCGCg- -3' miRNA: 3'- aCUUGaaGC-------------ACUUCGGUA---CCCGCGau -5' |
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| 18411 | 3' | -53.1 | NC_004681.1 | + | 21505 | 1.07 | 0.002659 |
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Target: 5'- gUGAACUUCGUGAAGCCAUGGGCGCUAu -3' miRNA: 3'- -ACUUGAAGCACUUCGGUACCCGCGAU- -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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