miRNA: 3'- -GGCGCuCGUGGCGg-------UCCAAGaGaaCC- -5'
miRNA: 3'- -GGCGCuCGUGGCGGUCCaa-----GAGaacc -5'
miRNA: 3'- ggCgCUCGUGGCGgUCCAAGa----------GAACC- -5'
miRNA: 3'- -GGCGCUCGUGGCGGUCCAAGAGAACC- -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 | |||||||
| 31339 | 3' | -56 | NC_006623.1 | + | 136891 | 0.66 | 0.929209 |
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Target: 5'- cCCGCGcGCGCUGCagaauuuaGGGUUC-CagGGa -3' miRNA: 3'- -GGCGCuCGUGGCGg-------UCCAAGaGaaCC- -5' |
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| 31339 | 3' | -56 | NC_006623.1 | + | 3880 | 0.66 | 0.923934 |
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Target: 5'- aCUGCG-GCACUGCUAGGggcgccgCUCa--- -3' miRNA: 3'- -GGCGCuCGUGGCGGUCCaa-----GAGaacc -5' |
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| 31339 | 3' | -56 | NC_006623.1 | + | 17036 | 0.7 | 0.726048 |
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Target: 5'- -gGgGAGCGCCGCaGGGUUCacaauauccagCUUGGg -3' miRNA: 3'- ggCgCUCGUGGCGgUCCAAGa----------GAACC- -5' |
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| 31339 | 3' | -56 | NC_006623.1 | + | 129890 | 1.12 | 0.001956 |
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Target: 5'- uCCGCGAGCACCGCCAGGUUCUCUUGGa -3' miRNA: 3'- -GGCGCUCGUGGCGGUCCAAGAGAACC- -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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