miRNA: 3'- ccaACGGAAAAUCaCAUUuCAGCUaa -5'
miRNA: 3'- -CCAACGGaaAAUC-AC-AUU-UCAGCUAA- -5'
miRNA: 3'- -CCAACGGAAAAu-----CACAUUUcagCUAa -5'
miRNA: 3'- -CCAACGGAAAAUCACAUUUCAGCUAA- -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 | |||||||
| 32279 | 5' | -42.6 | NC_007023.1 | + | 145196 | 0.67 | 1 |
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Target: 5'- --aUGCUUUUUAGgGUAAcGUCGAa- -3' miRNA: 3'- ccaACGGAAAAUCaCAUUuCAGCUaa -5' |
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| 32279 | 5' | -42.6 | NC_007023.1 | + | 79042 | 0.66 | 1 |
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Target: 5'- gGGUUGCCagUUAGuUGcUGGcAGUUGAUUg -3' miRNA: 3'- -CCAACGGaaAAUC-AC-AUU-UCAGCUAA- -5' |
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| 32279 | 5' | -42.6 | NC_007023.1 | + | 136835 | 0.69 | 0.999999 |
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Target: 5'- gGGUUGCCUUUUuuguuuGUGUAAAua-GAUa -3' miRNA: 3'- -CCAACGGAAAAu-----CACAUUUcagCUAa -5' |
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| 32279 | 5' | -42.6 | NC_007023.1 | + | 137012 | 1.11 | 0.055063 |
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Target: 5'- aGGUUGCCUUUUAGUGUAAAGUCGAUUa -3' miRNA: 3'- -CCAACGGAAAAUCACAUUUCAGCUAA- -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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