miRNA: 3'- -CGCaGGA-GUUACCAC----UGU--------UAGACGGC- -5'
miRNA: 3'- cgCAGgAGUUACCACU----GUuaGACGGC- -5'
miRNA: 3'- -CGCaGGAGUU------ACCAcUGuUAGACGGC- -5'
miRNA: 3'- -CGCaggaGUUACCACUGUUA---GACGGC- -5'
miRNA: 3'- -CGCAGGAGUUACCACUGUUAGACGGC- -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 | |||||||
| 1278 | 3' | -51.1 | NC_001317.1 | + | 9708 | 0.66 | 0.781436 |
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Target: 5'- cGCG-CCUcCGGUGGUGguucACAcaauauuuAUUUGCCGa -3' miRNA: 3'- -CGCaGGA-GUUACCAC----UGU--------UAGACGGC- -5' |
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| 1278 | 3' | -51.1 | NC_001317.1 | + | 7198 | 0.66 | 0.759784 |
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Target: 5'- -gGUCaUCAAUGGUGGuuucCAcgCUGUCGg -3' miRNA: 3'- cgCAGgAGUUACCACU----GUuaGACGGC- -5' |
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| 1278 | 3' | -51.1 | NC_001317.1 | + | 12887 | 0.68 | 0.644764 |
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Target: 5'- uGCGgCCUCAGcuucacUGGU-ACuGUCUGCCGc -3' miRNA: 3'- -CGCaGGAGUU------ACCAcUGuUAGACGGC- -5' |
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| 1278 | 3' | -51.1 | NC_001317.1 | + | 4708 | 0.69 | 0.632971 |
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Target: 5'- aGCGg---CGGUGGUGGCGAUgagCUGCUGa -3' miRNA: 3'- -CGCaggaGUUACCACUGUUA---GACGGC- -5' |
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| 1278 | 3' | -51.1 | NC_001317.1 | + | 2706 | 1.11 | 0.001016 |
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Target: 5'- gGCGUCCUCAAUGGUGACAAUCUGCCGc -3' miRNA: 3'- -CGCAGGAGUUACCACUGUUAGACGGC- -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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