miRNA: 3'- uCGGGACaAACGUUcGUCCCGcgcac -5'
miRNA: 3'- -UCGGGacaaaCGUUCG-UCCCGCGCac -5'
miRNA: 3'- -UCGGGa-----CAaaCGUUCGUCCCGcGcAC- -5'
miRNA: 3'- -UCGGGa--CAA-ACGUuCGU-CCCGCGCac -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 |
| Predicted miRNA align pattern | |||||||
| 12273 | 5' | -57.3 | NC_003309.1 | + | 53142 | 0.67 | 0.490626 |
|
Target: 5'- cGCCCUGcUUGCAAaCAGGGCu---- -3' miRNA: 3'- uCGGGACaAACGUUcGUCCCGcgcac -5' |
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| 12273 | 5' | -57.3 | NC_003309.1 | + | 25796 | 0.66 | 0.565223 |
|
Target: 5'- cAGCCUg----GCAAGUaAGGGUGCGg- -3' miRNA: 3'- -UCGGGacaaaCGUUCG-UCCCGCGCac -5' |
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| 12273 | 5' | -57.3 | NC_003309.1 | + | 22914 | 0.68 | 0.430522 |
|
Target: 5'- cGGCCCgccuacGUagGCAAGCAGGGC-CuUGg -3' miRNA: 3'- -UCGGGa-----CAaaCGUUCGUCCCGcGcAC- -5' |
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| 12273 | 5' | -57.3 | NC_003309.1 | + | 5085 | 0.69 | 0.357549 |
|
Target: 5'- gGGCCUucgGUUgUGCAuGCAcGGGCGCGg- -3' miRNA: 3'- -UCGGGa--CAA-ACGUuCGU-CCCGCGCac -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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