miRNA: 3'- -GGAACGC-----------AGG-GUGaua-UGCUUAGCua -5'
miRNA: 3'- gGAACGCa-------GGGUGAUAUGCUUAGCUA- -5'
miRNA: 3'- -GGAACGCA---GGGUGAu-AUGCuUAGCUA- -5'
miRNA: 3'- -GGAACGCAGGGUGAUAUGCUUAGCUA- -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 | |||||||
| 16688 | 5' | -49 | NC_004156.1 | + | 111704 | 0.66 | 0.999728 |
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Target: 5'- aCCUUGCGcguaaucagcuUCCaCACggugACGAAUCGu- -3' miRNA: 3'- -GGAACGC-----------AGG-GUGaua-UGCUUAGCua -5' |
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| 16688 | 5' | -49 | NC_004156.1 | + | 108275 | 0.68 | 0.998806 |
|
Target: 5'- gUUUGUGgcagaucgUCUACUGUACGAGUUGAUu -3' miRNA: 3'- gGAACGCa-------GGGUGAUAUGCUUAGCUA- -5' |
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| 16688 | 5' | -49 | NC_004156.1 | + | 183566 | 0.69 | 0.996575 |
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Target: 5'- aCCUUGUGUggcUCCGCUcuUGCG-AUCGAUg -3' miRNA: 3'- -GGAACGCA---GGGUGAu-AUGCuUAGCUA- -5' |
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| 16688 | 5' | -49 | NC_004156.1 | + | 145346 | 1.08 | 0.024842 |
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Target: 5'- gCCUUGCGUCCCACUAUACGAAUCGAUc -3' miRNA: 3'- -GGAACGCAGGGUGAUAUGCUUAGCUA- -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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