miRNA: 3'- -AGCGGaAGCA------------CGCGCU-CCACUUC-CUa -5'
miRNA: 3'- agCGGaAGCaCGCGCuCCACUU-CCUA- -5'
miRNA: 3'- aGCGGAAGCaCgCGCU-CCAC--------UUCCUa -5'
miRNA: 3'- -AGCGGAAGCACGCGCUCCACUUCCUA- -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 | |||||||
| 26682 | 5' | -56.4 | NC_005808.1 | + | 7824 | 0.66 | 0.554836 |
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Target: 5'- gUUGCCcUCGUugcccauguucaGCGCGAuGGUGAGGcGGg -3' miRNA: 3'- -AGCGGaAGCA------------CGCGCU-CCACUUC-CUa -5' |
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| 26682 | 5' | -56.4 | NC_005808.1 | + | 632 | 0.67 | 0.522217 |
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Target: 5'- -aGCC-UCG-GCGCG-GGUGAAcGGGUc -3' miRNA: 3'- agCGGaAGCaCGCGCuCCACUU-CCUA- -5' |
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| 26682 | 5' | -56.4 | NC_005808.1 | + | 36159 | 0.68 | 0.439424 |
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Target: 5'- aCGCCUUCGcGgGCGGuGGUGucgcgagcGAGGAc -3' miRNA: 3'- aGCGGAAGCaCgCGCU-CCAC--------UUCCUa -5' |
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| 26682 | 5' | -56.4 | NC_005808.1 | + | 25533 | 1.06 | 0.000904 |
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Target: 5'- uUCGCCUUCGUGCGCGAGGUGAAGGAUu -3' miRNA: 3'- -AGCGGAAGCACGCGCUCCACUUCCUA- -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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