miRNA: 3'- ccacAGUCGCGUacc--UUGCUUGGCAU- -5'
miRNA: 3'- ccacAGUCGCGU--ACCu-----UGCUUGGCAU- -5'
miRNA: 3'- -CCac-AGU---CGCGUACCu-UGCUUGGCAU- -5'
miRNA: 3'- -CCAC---AGUCGCGUa------CCUUGCUuGGCau -5'
miRNA: 3'- -CCACAGUCGCGUACCUUGCUUGGCAU- -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 | |||||||
| 16568 | 5' | -52.4 | NC_004117.1 | + | 72302 | 0.66 | 0.982496 |
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Target: 5'- ---aUCAGCGCAgaguuGAUGAACCGUGg -3' miRNA: 3'- ccacAGUCGCGUacc--UUGCUUGGCAU- -5' |
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| 16568 | 5' | -52.4 | NC_004117.1 | + | 71815 | 0.67 | 0.970067 |
|
Target: 5'- ---cUCGGCGCAucUGGucaaacACGGGCCGUGu -3' miRNA: 3'- ccacAGUCGCGU--ACCu-----UGCUUGGCAU- -5' |
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| 16568 | 5' | -52.4 | NC_004117.1 | + | 21780 | 0.67 | 0.963654 |
|
Target: 5'- cGGacaUCAuuuGUGCGUGGuuGCGGACCGUAa -3' miRNA: 3'- -CCac-AGU---CGCGUACCu-UGCUUGGCAU- -5' |
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| 16568 | 5' | -52.4 | NC_004117.1 | + | 151482 | 0.69 | 0.91141 |
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Target: 5'- gGGUGugcUCGGCGCAaacguaaGGAACGAuCCGa- -3' miRNA: 3'- -CCAC---AGUCGCGUa------CCUUGCUuGGCau -5' |
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| 16568 | 5' | -52.4 | NC_004117.1 | + | 19800 | 1.09 | 0.00631 |
|
Target: 5'- aGGUGUCAGCGCAUGGAACGAACCGUAc -3' miRNA: 3'- -CCACAGUCGCGUACCUUGCUUGGCAU- -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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