miRNA: 3'- aCgGUCCuCUuaUUUCAG-ACUAGUAa -5'
miRNA: 3'- -ACGGU---CCUCUUAUUUC----------AGACUAgUAA- -5'
miRNA: 3'- aCG-GuCCUCUUa------UUUCAGACUAGUaa -5'
miRNA: 3'- -ACGGUCCUCUUAUUUCAGACUAGUAA- -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 | |||||||
| 31541 | 5' | -46.5 | NC_006820.1 | + | 24813 | 0.67 | 0.999839 |
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Target: 5'- aGgCAGGuGGcgGGGGUCaUGAUCAUg -3' miRNA: 3'- aCgGUCCuCUuaUUUCAG-ACUAGUAa -5' |
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| 31541 | 5' | -46.5 | NC_006820.1 | + | 119396 | 0.7 | 0.997314 |
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Target: 5'- cUGCCAaacGGAGAAUAGAGgauucgaaccUCUGGUgGUUu -3' miRNA: 3'- -ACGGU---CCUCUUAUUUC----------AGACUAgUAA- -5' |
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| 31541 | 5' | -46.5 | NC_006820.1 | + | 82635 | 0.72 | 0.990531 |
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Target: 5'- gGCaCuGGAGAAcuauacgGAGGUCUGAUCAa- -3' miRNA: 3'- aCG-GuCCUCUUa------UUUCAGACUAGUaa -5' |
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| 31541 | 5' | -46.5 | NC_006820.1 | + | 82834 | 1.06 | 0.038136 |
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Target: 5'- gUGCCAGGAGAAUAAAGUCUGAUCAUUc -3' miRNA: 3'- -ACGGUCCUCUUAUUUCAGACUAGUAA- -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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