miRNA: 3'- -GGGCGGUCCGUCGCCAUGUUGGGGAC- -5'
miRNA: 3'- -GGGCGGuCCGUCGCCa------UgUUGGG-GAc -5'
miRNA: 3'- -GGGCGG--UCCGUcGCCAUGUUGGGgac -5'
Results 1 - 3 of 3 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 | |||||||
| 3333 | 3' | -60.1 | NC_001547.1 | + | 5506 | 1.1 | 0.000027 |
|
Target: 5'- gCCCGCCAGGCAGCGGUACAACCCCUGg -3' miRNA: 3'- -GGGCGGUCCGUCGCCAUGUUGGGGAC- -5' |
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| 3333 | 3' | -60.1 | NC_001547.1 | + | 5386 | 0.72 | 0.045941 |
|
Target: 5'- gCCCGCCuGGCAGCGGcaagaaaAgAGCCCaCUc -3' miRNA: 3'- -GGGCGGuCCGUCGCCa------UgUUGGG-GAc -5' |
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| 3333 | 3' | -60.1 | NC_001547.1 | + | 3718 | 0.72 | 0.047424 |
|
Target: 5'- uUCCGCCgcAGGCA-CGGUACGACCUg-- -3' miRNA: 3'- -GGGCGG--UCCGUcGCCAUGUUGGGgac -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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