miRNA: 3'- cUUUUCGGGaa--------CACCu------------UAGGGUG-AGG- -5'
miRNA: 3'- -CUUUUCgGGAACA-CCU----UAGGGUGa---GG- -5'
miRNA: 3'- -CUUUUCGGGAACACCUUAGGGUGAGG- -5'
Results 1 - 3 of 3 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 | |||||||
| 15613 | 5' | -50.1 | NC_004050.1 | + | 2729 | 0.66 | 0.171438 |
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Target: 5'- cGAAGGCCCaugaaaggagGUGGuggcggacccgccAUCCCACcUCCg -3' miRNA: 3'- cUUUUCGGGaa--------CACCu------------UAGGGUG-AGG- -5' |
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| 15613 | 5' | -50.1 | NC_004050.1 | + | 808 | 0.67 | 0.125441 |
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Target: 5'- aGGAAAGgCUUUGUcGGGuacgAUCCCGCggcgCCu -3' miRNA: 3'- -CUUUUCgGGAACA-CCU----UAGGGUGa---GG- -5' |
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| 15613 | 5' | -50.1 | NC_004050.1 | + | 2447 | 1.12 | 0.000021 |
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Target: 5'- gGAAAAGCCCUUGUGGAAUCCCACUCCc -3' miRNA: 3'- -CUUUUCGGGAACACCUUAGGGUGAGG- -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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