miRNA: 3'- -GCCUAUGC-CG-GCg--GCUAGGC-----CGCCGG- -5'
miRNA: 3'- gccuaUGC-CG-GCGGCuaGGCCGCCGG- -5'
miRNA: 3'- -GCCuaUGCCGGCGGCu----AGGC-------CGC-CGG- -5'
miRNA: 3'- -GCCUAUG-CCGgCGGcuAgg-CCGCCGG- -5'
Results 21 - 24 of 24 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 | |||||||
| 12132 | 3' | -61.9 | NC_003309.1 | + | 16007 | 0.67 | 0.35343 |
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Target: 5'- uCGGAUGCGaGCgCGaauUGGUCCGucggcGCGGCUg -3' miRNA: 3'- -GCCUAUGC-CG-GCg--GCUAGGC-----CGCCGG- -5' |
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| 12132 | 3' | -61.9 | NC_003309.1 | + | 43538 | 0.66 | 0.386358 |
|
Target: 5'- ----cACGcGCaCGCCG--UCGGCGGCCa -3' miRNA: 3'- gccuaUGC-CG-GCGGCuaGGCCGCCGG- -5' |
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| 12132 | 3' | -61.9 | NC_003309.1 | + | 10893 | 0.66 | 0.411463 |
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Target: 5'- gCGGucGCGGUCGCCGcgcguUCCGcucgcucGCGcGCCu -3' miRNA: 3'- -GCCuaUGCCGGCGGCu----AGGC-------CGC-CGG- -5' |
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| 12132 | 3' | -61.9 | NC_003309.1 | + | 36842 | 0.66 | 0.421247 |
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Target: 5'- uCGGAUAUgGGCgGCCuuUaagGGUGGCCa -3' miRNA: 3'- -GCCUAUG-CCGgCGGcuAgg-CCGCCGG- -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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