miRNA: 3'- uCCGGUauagaGUUGGUaUAGGCUUg -5'
miRNA: 3'- uCCGGUauAGAGUUGgUAU---------AGGCUUG- -5'
miRNA: 3'- -UCCGGUAUAG-AGUUGGUa-UAGGCUUG- -5'
miRNA: 3'- -UCCGGUAUAGAGUUGGUAUAGGCUUG- -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 | |||||||
| 811 | 3' | -48.4 | NC_000866.4 | + | 32466 | 0.66 | 0.999551 |
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Target: 5'- uGGCCAg----CAGCCG-AUCCGAGu -3' miRNA: 3'- uCCGGUauagaGUUGGUaUAGGCUUg -5' |
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| 811 | 3' | -48.4 | NC_000866.4 | + | 62349 | 0.66 | 0.999303 |
|
Target: 5'- uGGCCA--UUUCAAUgAUGgcacauagcUCCGAGCa -3' miRNA: 3'- uCCGGUauAGAGUUGgUAU---------AGGCUUG- -5' |
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| 811 | 3' | -48.4 | NC_000866.4 | + | 94209 | 0.76 | 0.8122 |
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Target: 5'- uAGGUCGUGUUgUCGGCCAagAUCCGAAUg -3' miRNA: 3'- -UCCGGUAUAG-AGUUGGUa-UAGGCUUG- -5' |
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| 811 | 3' | -48.4 | NC_000866.4 | + | 70897 | 1.12 | 0.010927 |
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Target: 5'- aAGGCCAUAUCUCAACCAUAUCCGAACg -3' miRNA: 3'- -UCCGGUAUAGAGUUGGUAUAGGCUUG- -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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