miRNA: 3'- -UGGGCGGCUAAGGGAUAGGGACUUGC- -5'
miRNA: 3'- ugGGCGGCU--AAGGg-------AUAGGGACUUGC- -5'
miRNA: 3'- -UGGGCG-GCUA---AGGGa----UAGGgaCUUGC- -5'
miRNA: 3'- -UGgGCGGCU-AAGGGAUAGGGAcUUGC- -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 | |||||||
| 1178 | 3' | -55.5 | NC_001132.2 | + | 158612 | 1.09 | 0.003395 |
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Target: 5'- gACCCGCCGAUUCCCUAUCCCUGAACGg -3' miRNA: 3'- -UGGGCGGCUAAGGGAUAGGGACUUGC- -5' |
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| 1178 | 3' | -55.5 | NC_001132.2 | + | 98056 | 0.7 | 0.738639 |
|
Target: 5'- -aCCGCCGGagUUCCaugcagcgUGUCUCUGAACGa -3' miRNA: 3'- ugGGCGGCU--AAGGg-------AUAGGGACUUGC- -5' |
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| 1178 | 3' | -55.5 | NC_001132.2 | + | 151000 | 0.68 | 0.86897 |
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Target: 5'- gGCCCGCaCGAUcucUCCCaagucGUCCg-GAACGa -3' miRNA: 3'- -UGGGCG-GCUA---AGGGa----UAGGgaCUUGC- -5' |
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| 1178 | 3' | -55.5 | NC_001132.2 | + | 96884 | 0.67 | 0.890109 |
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Target: 5'- aACaCGUCGAcUUCCUUAUCCCUuAACGc -3' miRNA: 3'- -UGgGCGGCU-AAGGGAUAGGGAcUUGC- -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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