miRNA: 3'- -GGCGGCGGacaCGGa-CGCCCGGacag -5'
miRNA: 3'- gGCGGCGGAca----CGGACgCCCGGacag -5'
miRNA: 3'- -GGCg-GCGgACACGGa-CGCCCG---GACAG- -5'
miRNA: 3'- ggC-GGCGGACaCGGAC----GCCCGGACAG- -5'
miRNA: 3'- -GGCGGCGGACACGGACGCCCGGACAG- -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 | |||||||
| 2716 | 5' | -63.8 | NC_001491.2 | + | 114428 | 0.69 | 0.397915 |
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Target: 5'- cCCGCCGCCga-GCCccGCGGGUCg--- -3' miRNA: 3'- -GGCGGCGGacaCGGa-CGCCCGGacag -5' |
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| 2716 | 5' | -63.8 | NC_001491.2 | + | 31785 | 0.69 | 0.374083 |
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Target: 5'- aUGCCGCCUauauucGCCUGgGGGCCa--- -3' miRNA: 3'- gGCGGCGGAca----CGGACgCCCGGacag -5' |
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| 2716 | 5' | -63.8 | NC_001491.2 | + | 85431 | 0.69 | 0.358741 |
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Target: 5'- gUCGgaCGCgUGUGCCccGCGGGCaccCUGUCg -3' miRNA: 3'- -GGCg-GCGgACACGGa-CGCCCG---GACAG- -5' |
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| 2716 | 5' | -63.8 | NC_001491.2 | + | 132521 | 0.71 | 0.295268 |
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Target: 5'- -gGuCCGCCUG-GCCUGguuuCGGGUCUGUUu -3' miRNA: 3'- ggC-GGCGGACaCGGAC----GCCCGGACAG- -5' |
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| 2716 | 5' | -63.8 | NC_001491.2 | + | 137359 | 1.1 | 0.000437 |
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Target: 5'- gCCGCCGCCUGUGCCUGCGGGCCUGUCg -3' miRNA: 3'- -GGCGGCGGACACGGACGCCCGGACAG- -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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