miRNA: 3'- gUGG-----UCCGga--UCCuaCC-UCGCCGUAG- -5'
miRNA: 3'- guGGUC-CGGAUCCua-CC-----UCGCCGUAg -5'
miRNA: 3'- -GUGGUCC------------GGAUCCU-ACC--UCGCCgUAG- -5'
miRNA: 3'- -GUGGUCCGGaUCCUACCUCGCCGUAG- -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 | |||||||
| 32075 | 5' | -58.3 | NC_007016.1 | + | 82619 | 0.66 | 0.755893 |
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Target: 5'- gACCaacguAGGCaaggGGGcgGGcAGCGGCAUUc -3' miRNA: 3'- gUGG-----UCCGga--UCCuaCC-UCGCCGUAG- -5' |
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| 32075 | 5' | -58.3 | NC_007016.1 | + | 104422 | 0.67 | 0.70644 |
|
Target: 5'- -cCCAGcGCCUGGGccaGGcgcgcGGCGGCAUg -3' miRNA: 3'- guGGUC-CGGAUCCua-CC-----UCGCCGUAg -5' |
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| 32075 | 5' | -58.3 | NC_007016.1 | + | 62932 | 0.69 | 0.583333 |
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Target: 5'- gCACCGGGaaucggcaacauCCUGGGAgUGGccGGCGGgGUCc -3' miRNA: 3'- -GUGGUCC------------GGAUCCU-ACC--UCGCCgUAG- -5' |
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| 32075 | 5' | -58.3 | NC_007016.1 | + | 15866 | 0.97 | 0.008773 |
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Target: 5'- gCACCAGGUCcAGGAUGGAGCGGCAUCg -3' miRNA: 3'- -GUGGUCCGGaUCCUACCUCGCCGUAG- -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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