miRNA: 3'- -UCACU-UGGUCUGUAUC---AUAgUGGUCa -5'
miRNA: 3'- -UCACUugGUCUGUAU-------------CA--UAGugGUCa -5'
miRNA: 3'- uCACUugGUCUGuaucAUAGUGGUca -5'
miRNA: 3'- -UCACUUGGUCUGUAUCAUAGUGGUCA- -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
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| Predicted miRNA align pattern | |||||||
| 31538 | 5' | -48 | NC_006820.1 | + | 181448 | 0.66 | 0.999886 |
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Target: 5'- uGGUGGcGCUGGAUAUAGaacUAUgGCCAGa -3' miRNA: 3'- -UCACU-UGGUCUGUAUC---AUAgUGGUCa -5' |
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| 31538 | 5' | -48 | NC_006820.1 | + | 75116 | 0.66 | 0.999848 |
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Target: 5'- aGGUGAugCAGACAUGauuaauuugcuauGUaaGUCugCGGc -3' miRNA: 3'- -UCACUugGUCUGUAU-------------CA--UAGugGUCa -5' |
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| 31538 | 5' | -48 | NC_006820.1 | + | 6243 | 0.67 | 0.999508 |
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Target: 5'- cGUGAugCAGACcac-UAUCACCAa- -3' miRNA: 3'- uCACUugGUCUGuaucAUAGUGGUca -5' |
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| 31538 | 5' | -48 | NC_006820.1 | + | 62294 | 1.08 | 0.023264 |
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Target: 5'- gAGUGAACCAGACAUAGUAUCACCAGUc -3' miRNA: 3'- -UCACUUGGUCUGUAUCAUAGUGGUCA- -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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