miRNA: 3'- -AUUUGAGG-------GCGUGGGC-GAG--UGACAGa -5'
miRNA: 3'- auUUGaGGGCGUGGGCGagu----GACAGa -5'
miRNA: 3'- auuuGAGGGCGUGGgCGagUGACAGA- -5'
miRNA: 3'- aUUUGAGG-GCGu---GggCGaGUGACAGA- -5'
miRNA: 3'- -AUUUGAGGGCGUGGGCGAGUGACAGA- -5'
Results 1 - 5 of 5 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 | |||||||
| 9483 | 3' | -55.6 | NC_002531.1 | + | 87610 | 0.66 | 0.875591 |
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Target: 5'- uUGAACUCUauaguggUGCACUCGuCUCcuACUGUCa -3' miRNA: 3'- -AUUUGAGG-------GCGUGGGC-GAG--UGACAGa -5' |
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| 9483 | 3' | -55.6 | NC_002531.1 | + | 30292 | 0.67 | 0.845079 |
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Target: 5'- -uAAC-CCCGCAUCCGCgaacuauCUGUCc -3' miRNA: 3'- auUUGaGGGCGUGGGCGagu----GACAGa -5' |
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| 9483 | 3' | -55.6 | NC_002531.1 | + | 49794 | 0.67 | 0.810587 |
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Target: 5'- ---uCUCCUGCACCaGCagGCUGUUUa -3' miRNA: 3'- auuuGAGGGCGUGGgCGagUGACAGA- -5' |
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| 9483 | 3' | -55.6 | NC_002531.1 | + | 44933 | 0.7 | 0.651573 |
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Target: 5'- gAAACUCCuCGCugguCuuGCcCACUGUCUu -3' miRNA: 3'- aUUUGAGG-GCGu---GggCGaGUGACAGA- -5' |
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| 9483 | 3' | -55.6 | NC_002531.1 | + | 30166 | 1.07 | 0.003318 |
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Target: 5'- uUAAACUCCCGCACCCGCUCACUGUCUg -3' miRNA: 3'- -AUUUGAGGGCGUGGGCGAGUGACAGA- -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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