miRNA: 3'- gUCUAGGUCcC--------AGUGGCGGAGuGAGa -5'
miRNA: 3'- -GUCUaggUCCCAGUGGCGGa------GUGAGa -5'
miRNA: 3'- -GUCU--AGGU-C-CCAGUGGCGGa------GUGAGa -5'
miRNA: 3'- gucuAGGUCCCAG----UgGCGGAGUGAGa -5'
miRNA: 3'- -GUCUAGGUCCCAGUGGCGGAGUGAGA- -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 | |||||||
| 13330 | 3' | -57.2 | NC_003409.1 | + | 43799 | 0.66 | 0.850826 |
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Target: 5'- gAGAUUCAGaGaacccgcaUCGCCGCCUCuCUCg -3' miRNA: 3'- gUCUAGGUCcC--------AGUGGCGGAGuGAGa -5' |
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| 13330 | 3' | -57.2 | NC_003409.1 | + | 95371 | 0.69 | 0.693999 |
|
Target: 5'- aCAGAaagGGGGUCGCCGCCaacguccCGCUCa -3' miRNA: 3'- -GUCUaggUCCCAGUGGCGGa------GUGAGa -5' |
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| 13330 | 3' | -57.2 | NC_003409.1 | + | 110571 | 0.7 | 0.612222 |
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Target: 5'- uCAGAaaUCCAcGaGGUCGCCGCCacgccgcCACUCa -3' miRNA: 3'- -GUCU--AGGU-C-CCAGUGGCGGa------GUGAGa -5' |
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| 13330 | 3' | -57.2 | NC_003409.1 | + | 110513 | 0.71 | 0.531326 |
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Target: 5'- ---cUCCAGGGUUcccgAgCGCCUCGCUCc -3' miRNA: 3'- gucuAGGUCCCAG----UgGCGGAGUGAGa -5' |
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| 13330 | 3' | -57.2 | NC_003409.1 | + | 97974 | 1.08 | 0.002352 |
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Target: 5'- gCAGAUCCAGGGUCACCGCCUCACUCUg -3' miRNA: 3'- -GUCUAGGUCCCAGUGGCGGAGUGAGA- -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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