miRNA: 3'- augaACUCCUCCa--------------AUUUGCCCUG-CAA- -5'
miRNA: 3'- aUGaaCUCCUCCAauuUGCCCUG-CAa -5'
miRNA: 3'- auGAACUCCUCCAAUUUG--CCCugCaa -5'
miRNA: 3'- -AUGAACUCCUCCAAUUUGCCCUGCAA- -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 | |||||||
| 28386 | 3' | -50 | NC_005946.1 | + | 3680 | 0.66 | 0.981728 |
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Target: 5'- ---gUGAGGAGGauguuacucaucuggUAGACGGGGCuGUUu -3' miRNA: 3'- augaACUCCUCCa--------------AUUUGCCCUG-CAA- -5' |
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| 28386 | 3' | -50 | NC_005946.1 | + | 71824 | 0.72 | 0.820089 |
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Target: 5'- gACggGAGGAGGUcccGCGGGACuGUg -3' miRNA: 3'- aUGaaCUCCUCCAauuUGCCCUG-CAa -5' |
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| 28386 | 3' | -50 | NC_005946.1 | + | 24705 | 0.72 | 0.801091 |
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Target: 5'- -gUUUGGGGGGGUUGGGCccGGGugGg- -3' miRNA: 3'- auGAACUCCUCCAAUUUG--CCCugCaa -5' |
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| 28386 | 3' | -50 | NC_005946.1 | + | 48742 | 1.05 | 0.011777 |
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Target: 5'- gUACUUGAGGAGGUUAAACGGGACGUUg -3' miRNA: 3'- -AUGAACUCCUCCAAUUUGCCCUGCAA- -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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