miRNA: 3'- gCGCCGUCUACCA---GGUCUauGGGCau -5'
miRNA: 3'- gCGCCGUCUAC-CAGG--------------UCUAUGGGCAU- -5'
miRNA: 3'- -GCGC-CGUCU-------------ACCAGGUC---UAUGGGCau -5'
miRNA: 3'- gCGCCguCUACCAGGUCUAUGgGCAu -5'
miRNA: 3'- -GCGCCGUCUACCAGGUCUAUGGGCAU- -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 |
| Predicted miRNA align pattern | |||||||
| 21739 | 5' | -56.4 | NC_004813.1 | + | 27211 | 0.74 | 0.227372 |
|
Target: 5'- aGCGGCGGGUGGUaugCCGGA--CCCGa- -3' miRNA: 3'- gCGCCGUCUACCA---GGUCUauGGGCau -5' |
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| 21739 | 5' | -56.4 | NC_004813.1 | + | 41867 | 0.71 | 0.354014 |
|
Target: 5'- gGUGGCGGAUGaGUUCgacaaccccaccacGGAUAUCCGUAa -3' miRNA: 3'- gCGCCGUCUAC-CAGG--------------UCUAUGGGCAU- -5' |
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| 21739 | 5' | -56.4 | NC_004813.1 | + | 37276 | 0.69 | 0.486738 |
|
Target: 5'- cCGUGaGCAGGugcuggccgucuaUGGUCCGGuacAUGCCCGg- -3' miRNA: 3'- -GCGC-CGUCU-------------ACCAGGUC---UAUGGGCau -5' |
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| 21739 | 5' | -56.4 | NC_004813.1 | + | 28673 | 0.77 | 0.148014 |
|
Target: 5'- uGUGGguGAUGGUCCGGAUAUgUGUc -3' miRNA: 3'- gCGCCguCUACCAGGUCUAUGgGCAu -5' |
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| 21739 | 5' | -56.4 | NC_004813.1 | + | 24521 | 1.07 | 0.001142 |
|
Target: 5'- cCGCGGCAGAUGGUCCAGAUACCCGUAc -3' miRNA: 3'- -GCGCCGUCUACCAGGUCUAUGGGCAU- -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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