miRNA: 3'- -CGCGGaUGU-GCGCUgAC-CuuCCUGUu -5'
miRNA: 3'- -CGC-GGAUGUgCGCuGaCCUUC-CUGUU- -5'
miRNA: 3'- -CGCGGAUGUG----CGCUGaCCUUCc-UGUu -5'
miRNA: 3'- -CGCGGAUGUGCGCUGACCUUCCUGUU- -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 | |||||||
| 4322 | 3' | -55.1 | NC_001720.1 | + | 18020 | 0.66 | 0.602099 |
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Target: 5'- gGCGCCgGCGcCGCGGgUGcGgcGGGCGg -3' miRNA: 3'- -CGCGGaUGU-GCGCUgAC-CuuCCUGUu -5' |
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| 4322 | 3' | -55.1 | NC_001720.1 | + | 13332 | 0.67 | 0.590848 |
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Target: 5'- uGCGcCCUACGgGCGuCaGGAGGuGGCGGa -3' miRNA: 3'- -CGC-GGAUGUgCGCuGaCCUUC-CUGUU- -5' |
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| 4322 | 3' | -55.1 | NC_001720.1 | + | 18166 | 0.68 | 0.524417 |
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Target: 5'- uGCGCCUGCGCuuggGCGGC-GGAGGucGCAu -3' miRNA: 3'- -CGCGGAUGUG----CGCUGaCCUUCc-UGUu -5' |
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| 4322 | 3' | -55.1 | NC_001720.1 | + | 3066 | 1.08 | 0.00081 |
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Target: 5'- gGCGCCUACACGCGACUGGAAGGACAAa -3' miRNA: 3'- -CGCGGAUGUGCGCUGACCUUCCUGUU- -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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