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miRNA: 3'- -AACA---AG--UCGUGAGUACGCGuCAgUGa -5'
miRNA: 3'- aacaaguCGUGAGUACGCGUCa----GUGA- -5'
miRNA: 3'- aACaa-GUCGUGa-GUaCGCGUCAGUGA- -5'
miRNA: 3'- -AACAAGUCGUGAGUACGCGUCAGUGA- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 12323 | 5' | -52 | NC_003324.1 | + | 1041 | 0.67 | 0.789232 |
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Target: 5'- cUUGUcugUCagAGCACUCAUGCGCcGUgAUa -3' miRNA: 3'- -AACA---AG--UCGUGAGUACGCGuCAgUGa -5' |
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| 12323 | 5' | -52 | NC_003324.1 | + | 32689 | 0.68 | 0.724768 |
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Target: 5'- ------cGCACUCAUGCGCGGaacgaCACUg -3' miRNA: 3'- aacaaguCGUGAGUACGCGUCa----GUGA- -5' |
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| 12323 | 5' | -52 | NC_003324.1 | + | 27103 | 0.7 | 0.599082 |
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Target: 5'- cUGgcgCAGCACacCA-GCGCGGUCGCUc -3' miRNA: 3'- aACaa-GUCGUGa-GUaCGCGUCAGUGA- -5' |
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| 12323 | 5' | -52 | NC_003324.1 | + | 4021 | 1.06 | 0.002446 |
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Target: 5'- aUUGUUCAGCACUCAUGCGCAGUCACUg -3' miRNA: 3'- -AACAAGUCGUGAGUACGCGUCAGUGA- -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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