miRNA: 3'- -UCAUAU------UGGAGUAUgUUu-GGUAGUCg -5'
miRNA: 3'- ucaUAUUGGAGUA--UGUuu--GGUAG--------UCG- -5'
miRNA: 3'- -UCAUA--UUggAGUAUGUu--UGGUAGUCG- -5'
miRNA: 3'- -UCAUAUUGGAGUAUGUUUGGUAGUCG- -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 | |||||||
| 27502 | 5' | -43.1 | NC_005876.1 | + | 9234 | 0.66 | 0.910779 |
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Target: 5'- uAGUGUAccggguACCUUGUGgAAuuCCAUCAGg -3' miRNA: 3'- -UCAUAU------UGGAGUAUgUUu-GGUAGUCg -5' |
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| 27502 | 5' | -43.1 | NC_005876.1 | + | 6463 | 0.66 | 0.902518 |
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Target: 5'- --cAUAACCUCAUaaGCAugauCCAUCucagguuuAGCa -3' miRNA: 3'- ucaUAUUGGAGUA--UGUuu--GGUAG--------UCG- -5' |
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| 27502 | 5' | -43.1 | NC_005876.1 | + | 3774 | 0.67 | 0.884745 |
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Target: 5'- cAGUAUggGAagUCAUGCGugcACCAUUGGCa -3' miRNA: 3'- -UCAUA--UUggAGUAUGUu--UGGUAGUCG- -5' |
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| 27502 | 5' | -43.1 | NC_005876.1 | + | 8037 | 1.16 | 0.00079 |
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Target: 5'- aAGUAUAACCUCAUACAAACCAUCAGCg -3' miRNA: 3'- -UCAUAUUGGAGUAUGUUUGGUAGUCG- -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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