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miRNA: 3'- -CGcGGGAAAAUGGAAA--CGU-------------UUCCAUU- -5'
miRNA: 3'- cGCGGGAAAAUGGAAA-----------CGUUU--CCAUu -5'
miRNA: 3'- -CGCGGGAAAAUGGaAACGUUUCCAUU- -5'
miRNA: 3'- -CGCGGGAAAAUGGAAACGUUUCCAUU- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 32375 | 5' | -46.6 | NC_007038.1 | + | 2366 | 0.69 | 0.645297 |
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Target: 5'- uGCaCCCUUUUACCUUUcaGUAguaauuuuuuugaAAGGUGAa -3' miRNA: 3'- -CGcGGGAAAAUGGAAA--CGU-------------UUCCAUU- -5' |
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| 32375 | 5' | -46.6 | NC_007038.1 | + | 2102 | 0.72 | 0.467778 |
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Target: 5'- aCGCCCUUUUACCUUUcaauuuuaagcGUAAAauGGUGu -3' miRNA: 3'- cGCGGGAAAAUGGAAA-----------CGUUU--CCAUu -5' |
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| 32375 | 5' | -46.6 | NC_007038.1 | + | 1983 | 1 | 0.006037 |
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Target: 5'- uGCGCCCUUUUACC-UUGCAAAGGUAAa -3' miRNA: 3'- -CGCGGGAAAAUGGaAACGUUUCCAUU- -5' |
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| 32375 | 5' | -46.6 | NC_007038.1 | + | 2032 | 1.1 | 0.001128 |
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Target: 5'- uGCGCCCUUUUACCUUUGCAAAGGUAAa -3' miRNA: 3'- -CGCGGGAAAAUGGAAACGUUUCCAUU- -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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