miRNA: 3'- gGGGCGcUAACCuCGCUGUA-GCAGCU- -5'
miRNA: 3'- -GGGGCGCUa----ACCUCGCuGU---AGCAGcu -5'
miRNA: 3'- gggGCGCua-ACCUCGCUGuaGC-AGCU- -5'
miRNA: 3'- -GG-GGCGCuaa-----CCUCGCUGUaGCAGcu -5'
miRNA: 3'- -GGGGCGCUAACCUCGCUGUAGCAGCU- -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 | |||||||
| 12369 | 3' | -54.9 | NC_003324.1 | + | 28470 | 0.66 | 0.802395 |
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Target: 5'- gCCCGCuGUUGG-GCGGUAUcCGUUGGa -3' miRNA: 3'- gGGGCGcUAACCuCGCUGUA-GCAGCU- -5' |
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| 12369 | 3' | -54.9 | NC_003324.1 | + | 23140 | 0.67 | 0.71185 |
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Target: 5'- aCCUCGUGGgacagUGGGGCGcCGauuUCGUCa- -3' miRNA: 3'- -GGGGCGCUa----ACCUCGCuGU---AGCAGcu -5' |
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| 12369 | 3' | -54.9 | NC_003324.1 | + | 25858 | 0.68 | 0.647576 |
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Target: 5'- --gCGCGuggUGGAGCGAUcgCGaUCGAc -3' miRNA: 3'- gggGCGCua-ACCUCGCUGuaGC-AGCU- -5' |
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| 12369 | 3' | -54.9 | NC_003324.1 | + | 22222 | 0.7 | 0.561413 |
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Target: 5'- gCCgCCGCGcaccuucgGGAGCGGCAaCGUCu- -3' miRNA: 3'- -GG-GGCGCuaa-----CCUCGCUGUaGCAGcu -5' |
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| 12369 | 3' | -54.9 | NC_003324.1 | + | 32590 | 1.1 | 0.001165 |
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Target: 5'- gCCCCGCGAUUGGAGCGACAUCGUCGAc -3' miRNA: 3'- -GGGGCGCUAACCUCGCUGUAGCAGCU- -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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