miRNA: 3'- -UCGUCGCacaAGAGGGGG-GCuGGCCC- -5'
miRNA: 3'- -UCGUCgCACAAgAGGGGGGCUg---GCCC- -5'
miRNA: 3'- -UCGUC-GCACaaGA--------GGGGGGCugGCCc -5'
miRNA: 3'- -UCGUCGCac--------AAGA----GGGGGGCUGGCCC- -5'
miRNA: 3'- -UCGUCGCACAAGAGGGGGGCUGGCCC- -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 | |||||||
| 11885 | 3' | -60.7 | NC_003266.2 | + | 17865 | 0.69 | 0.235509 |
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Target: 5'- cAGCAGCG---UCUCCUCCgCG-UCGGGa -3' miRNA: 3'- -UCGUCGCacaAGAGGGGG-GCuGGCCC- -5' |
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| 11885 | 3' | -60.7 | NC_003266.2 | + | 18500 | 0.69 | 0.212306 |
|
Target: 5'- gAGUAG-GUGUUgUCCUCCCGGuccaCGGGc -3' miRNA: 3'- -UCGUCgCACAAgAGGGGGGCUg---GCCC- -5' |
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| 11885 | 3' | -60.7 | NC_003266.2 | + | 23003 | 0.73 | 0.104883 |
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Target: 5'- uGGCGGcCGUGggCUucagcuacCCCCCCGugCGGa -3' miRNA: 3'- -UCGUC-GCACaaGA--------GGGGGGCugGCCc -5' |
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| 11885 | 3' | -60.7 | NC_003266.2 | + | 5908 | 0.76 | 0.063065 |
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Target: 5'- gAGCAGCGgcccgcccccUUUUauacCCCCCCGGCCGGGa -3' miRNA: 3'- -UCGUCGCac--------AAGA----GGGGGGCUGGCCC- -5' |
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| 11885 | 3' | -60.7 | NC_003266.2 | + | 13198 | 1.09 | 0.000189 |
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Target: 5'- cAGCAGCGUGUUCUCCCCCCGACCGGGu -3' miRNA: 3'- -UCGUCGCACAAGAGGGGGGCUGGCCC- -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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