miRNA: 3'- aGCUUucucUGGCGCUGCu--UCUGCGC- -5'
miRNA: 3'- aGCUuUCUCUGGCGCUGc--UUCUG--CGC- -5'
miRNA: 3'- -AGCUUUCUCUGG----------CGCUGCU--------UCUgCGC- -5'
miRNA: 3'- -AGCUUUCUCUGGCGCUGCUUCUGCGC- -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 | |||||||
| 6019 | 5' | -52.5 | NC_001809.1 | + | 6471 | 0.66 | 0.427574 |
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Target: 5'- cCGAA----GCUGCGACGcccAGACGCGu -3' miRNA: 3'- aGCUUucucUGGCGCUGCu--UCUGCGC- -5' |
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| 6019 | 5' | -52.5 | NC_001809.1 | + | 7479 | 0.66 | 0.406212 |
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Target: 5'- aUGAcAGAGGCUGCGGCuguGGGGCugGCGg -3' miRNA: 3'- aGCUuUCUCUGGCGCUGc--UUCUG--CGC- -5' |
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| 6019 | 5' | -52.5 | NC_001809.1 | + | 3584 | 0.68 | 0.336971 |
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Target: 5'- uUCGGAGGAGACCuucuacaggaGUGACGGucguauggGGAgGUGu -3' miRNA: 3'- -AGCUUUCUCUGG----------CGCUGCU--------UCUgCGC- -5' |
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| 6019 | 5' | -52.5 | NC_001809.1 | + | 183 | 1.09 | 0.000234 |
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Target: 5'- gUCGAAAGAGACCGCGACGAAGACGCGu -3' miRNA: 3'- -AGCUUUCUCUGGCGCUGCUUCUGCGC- -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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