miRNA: 3'- ccACCACGUaAGC-C-----------UCG-CGCUGCUAG- -5'
miRNA: 3'- cCACCa-CGUAAGCC--UCGCGcuGCUAg -5'
miRNA: 3'- ccaCCACGUaa--GCCu---CGCGCUGCUAg -5'
miRNA: 3'- -CCACCACGuaagCCUCGcg-CUGCUAG- -5'
miRNA: 3'- -CCACCACGUAAGCCUCGCGCUGCUAG- -5'
Results 1 - 5 of 5 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 | |||||||
| 14703 | 3' | -54.5 | NC_003529.1 | + | 100489 | 0.66 | 0.960396 |
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Target: 5'- -uUGGUGCG-UCGcGucaacaucaucAGCaGCGGCGAUCg -3' miRNA: 3'- ccACCACGUaAGC-C-----------UCG-CGCUGCUAG- -5' |
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| 14703 | 3' | -54.5 | NC_003529.1 | + | 35597 | 0.66 | 0.94867 |
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Target: 5'- cGUGGccGCGUUCGGccAGCGCcuCGAUg -3' miRNA: 3'- cCACCa-CGUAAGCC--UCGCGcuGCUAg -5' |
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| 14703 | 3' | -54.5 | NC_003529.1 | + | 120032 | 0.67 | 0.934844 |
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Target: 5'- --cGGUGCGgcaaCGGugacGCGUGACGGUa -3' miRNA: 3'- ccaCCACGUaa--GCCu---CGCGCUGCUAg -5' |
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| 14703 | 3' | -54.5 | NC_003529.1 | + | 1587 | 0.68 | 0.880488 |
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Target: 5'- uGGUGGUGCcg--GGGGCaaaGAUGGUCg -3' miRNA: 3'- -CCACCACGuaagCCUCGcg-CUGCUAG- -5' |
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| 14703 | 3' | -54.5 | NC_003529.1 | + | 58296 | 1.11 | 0.003006 |
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Target: 5'- uGGUGGUGCAUUCGGAGCGCGACGAUCu -3' miRNA: 3'- -CCACCACGUAAGCCUCGCGCUGCUAG- -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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