miRNA: 3'- -UGCUGGACuu---------CGGG-GCGuCCGUCUUa -5'
miRNA: 3'- -UGcUGGAcuuc--GGGGCGUCCGUCUUa -5'
miRNA: 3'- -UGCuGGACU-------UCGGGGCGU-CCGUcuua -5'
miRNA: 3'- -UGCUGGACUUCGGGGCGUCCGUCUUA- -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 | |||||||
| 12732 | 5' | -58.2 | NC_003356.1 | + | 31863 | 0.66 | 0.411449 |
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Target: 5'- cGCGACCUGucaacagaacuGCCCaUGUcGGCGGAAg -3' miRNA: 3'- -UGCUGGACuu---------CGGG-GCGuCCGUCUUa -5' |
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| 12732 | 5' | -58.2 | NC_003356.1 | + | 19560 | 0.68 | 0.34168 |
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Target: 5'- uGCcGCCUccuccaCCCCGCAGGCGGGAg -3' miRNA: 3'- -UGcUGGAcuuc--GGGGCGUCCGUCUUa -5' |
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| 12732 | 5' | -58.2 | NC_003356.1 | + | 9210 | 0.7 | 0.232041 |
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Target: 5'- aGCGuCCUGAaucgcgaAGCCCCGCAuGGCGu--- -3' miRNA: 3'- -UGCuGGACU-------UCGGGGCGU-CCGUcuua -5' |
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| 12732 | 5' | -58.2 | NC_003356.1 | + | 29966 | 1.04 | 0.00062 |
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Target: 5'- cACGACCUGAAGCCCCGCAGGCAGAAUc -3' miRNA: 3'- -UGCUGGACUUCGGGGCGUCCGUCUUA- -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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