miRNA: 3'- aGUACAUCAuGGGCAUgugCUCUCuG- -5'
miRNA: 3'- -AGUA-CAUCAUGGGCAUgUGcuc-UCUG- -5'
miRNA: 3'- aguaCAUCAUGGGCaUGUGCUC---UCUG- -5'
miRNA: 3'- -AGUACAUCAUGGGCAUGUGCUCUCUG- -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 | |||||||
| 28382 | 3' | -49.7 | NC_005946.1 | + | 8722 | 0.68 | 0.976667 |
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Target: 5'- cCAUGUGGUcCCCGUGa--GAGGGcCu -3' miRNA: 3'- aGUACAUCAuGGGCAUgugCUCUCuG- -5' |
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| 28382 | 3' | -49.7 | NC_005946.1 | + | 4986 | 0.68 | 0.967854 |
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Target: 5'- gUCGUaGUAGUACCCGUAgGCcaucAGGCc -3' miRNA: 3'- -AGUA-CAUCAUGGGCAUgUGcuc-UCUG- -5' |
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| 28382 | 3' | -49.7 | NC_005946.1 | + | 37186 | 0.73 | 0.823739 |
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Target: 5'- ---cGUGGUACCUGcACACGGGgucGGACg -3' miRNA: 3'- aguaCAUCAUGGGCaUGUGCUC---UCUG- -5' |
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| 28382 | 3' | -49.7 | NC_005946.1 | + | 45909 | 1.12 | 0.005437 |
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Target: 5'- cUCAUGUAGUACCCGUACACGAGAGACa -3' miRNA: 3'- -AGUACAUCAUGGGCAUGUGCUCUCUG- -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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