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miRNA: 3'- uuucUUCCUGUa---CCUG--GUUGU-CCGGG- -5'
miRNA: 3'- -UUUCUUC--CUGUACCUG-GUu----GUCCGGG- -5'
miRNA: 3'- -UUUCUUCCUGUACCUGGUUGUCCGGG- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 22213 | 5' | -52.5 | NC_005031.1 | + | 410 | 0.66 | 0.099772 |
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Target: 5'- ---cGAGGACAguggGGGCagCAGCAcGGCUCa -3' miRNA: 3'- uuucUUCCUGUa---CCUG--GUUGU-CCGGG- -5' |
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| 22213 | 5' | -52.5 | NC_005031.1 | + | 1934 | 0.68 | 0.056728 |
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Target: 5'- cAGGGAAGacGAUGUGGGCuCGuucuuUAGGCCCa -3' miRNA: 3'- -UUUCUUC--CUGUACCUG-GUu----GUCCGGG- -5' |
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| 22213 | 5' | -52.5 | NC_005031.1 | + | 417 | 1.11 | 0.00001 |
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Target: 5'- aAAAGAAGGACAUGGACCAACAGGCCCa -3' miRNA: 3'- -UUUCUUCCUGUACCUGGUUGUCCGGG- -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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