miRNA: 3'- -AGUCCACgUa-------GUGGA---AACGUGUaaac -5'
miRNA: 3'- aGUCCaCGUAg--UGGAaa---CGUGUAAAC- -5'
miRNA: 3'- aGUCC---ACGUAGUGGAaaC-GUGUAAAc -5'
miRNA: 3'- -AGUCCACGUAGUGGAAACGUGUAAAC- -5'
miRNA: 3'- -AGUCCACGUAGUGGAAACGUGUAAAC- -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 | |||||||
| 29115 | 5' | -47.5 | NC_006146.1 | + | 11475 | 0.66 | 0.999828 |
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Target: 5'- aUCGGGUGgAguuuauugCGCCUaguUUGCGCAa--- -3' miRNA: 3'- -AGUCCACgUa-------GUGGA---AACGUGUaaac -5' |
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| 29115 | 5' | -47.5 | NC_006146.1 | + | 88795 | 0.66 | 0.99964 |
|
Target: 5'- aCAGG-GCGUggaGCCUgcuggGCAUGUUUGg -3' miRNA: 3'- aGUCCaCGUAg--UGGAaa---CGUGUAAAC- -5' |
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| 29115 | 5' | -47.5 | NC_006146.1 | + | 166284 | 0.68 | 0.998068 |
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Target: 5'- gCAGGgucUGCAUCACCUcgGuCAUGUUUc -3' miRNA: 3'- aGUCC---ACGUAGUGGAaaC-GUGUAAAc -5' |
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| 29115 | 5' | -47.5 | NC_006146.1 | + | 34982 | 1.1 | 0.016657 |
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Target: 5'- uUCGGGUGCAUCACCUUUGCACAUUUGg -3' miRNA: 3'- -AGUCCACGUAGUGGAAACGUGUAAAC- -5' |
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| 29115 | 5' | -47.5 | NC_006146.1 | + | 138812 | 1.11 | 0.013547 |
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Target: 5'- uUCAGGUGCAUCACCUUUGCACAUUUGg -3' miRNA: 3'- -AGUCCACGUAGUGGAAACGUGUAAAC- -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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