miRNA: 3'- -CCUG--CC-CGA--------------GACCCUACUgGGGCUuu -5'
miRNA: 3'- -CCUgCCCGAGA--------------CCCua-------------CUGGGGCUUU- -5'
miRNA: 3'- -CCUGC-----CCgAGACCCuACUGGGgCUUU- -5'
miRNA: 3'- -CCUGCCCGAGACCCUACUGGGGCUUU- -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 | |||||||
| 6311 | 3' | -58.3 | NC_001844.1 | + | 113259 | 0.66 | 0.822572 |
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Target: 5'- gGGACguGGaGCUgguugcagaucaccCUGGGGUGAgCCCGGc- -3' miRNA: 3'- -CCUG--CC-CGA--------------GACCCUACUgGGGCUuu -5' |
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| 6311 | 3' | -58.3 | NC_001844.1 | + | 143398 | 0.66 | 0.793837 |
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Target: 5'- aGGA-GGGCUCUcuaccggagcgaccGGGucguauccuccgcggGACCCCGGGAg -3' miRNA: 3'- -CCUgCCCGAGA--------------CCCua-------------CUGGGGCUUU- -5' |
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| 6311 | 3' | -58.3 | NC_001844.1 | + | 143155 | 0.68 | 0.694589 |
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Target: 5'- gGGGCGagccuGGgUCUGGG-UGGCCCgGGAGc -3' miRNA: 3'- -CCUGC-----CCgAGACCCuACUGGGgCUUU- -5' |
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| 6311 | 3' | -58.3 | NC_001844.1 | + | 116238 | 1.07 | 0.002114 |
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Target: 5'- gGGACGGGCUCUGGGAUGACCCCGAAAu -3' miRNA: 3'- -CCUGCCCGAGACCCUACUGGGGCUUU- -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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