miRNA: 3'- cUUGAAGUuuaa-----GUUcACAUUCCGUC- -5'
miRNA: 3'- -CUUGAAGUUu--AAGuuc---ACAuUCCGUC- -5'
miRNA: 3'- cUUGAAGUUUAAGu-UCACAUU-----CCGUc -5'
miRNA: 3'- cuugaAGUUUAAGUUCaCAUUCCGUC- -5'
miRNA: 3'- -CUUGAAGUUUAAGUUCACAUUCCGUC- -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 | |||||||
| 22838 | 5' | -42 | NC_005135.1 | + | 100867 | 0.66 | 1 |
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Target: 5'- aAACUUCAuacaaacucCAAaUGUAAGGCAGc -3' miRNA: 3'- cUUGAAGUuuaa-----GUUcACAUUCCGUC- -5' |
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| 22838 | 5' | -42 | NC_005135.1 | + | 38877 | 0.66 | 1 |
|
Target: 5'- aGAGCUUCAAuguUUCuacgcaUGUuGGGCAGc -3' miRNA: 3'- -CUUGAAGUUu--AAGuuc---ACAuUCCGUC- -5' |
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| 22838 | 5' | -42 | NC_005135.1 | + | 25993 | 0.66 | 1 |
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Target: 5'- uAACUUCGAAUUUccGGUGUGGuuuguGGCAa -3' miRNA: 3'- cUUGAAGUUUAAGu-UCACAUU-----CCGUc -5' |
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| 22838 | 5' | -42 | NC_005135.1 | + | 141236 | 0.8 | 0.957978 |
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Target: 5'- ----gUCGAAUUCGAGgGUAGGGCAGa -3' miRNA: 3'- cuugaAGUUUAAGUUCaCAUUCCGUC- -5' |
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| 22838 | 5' | -42 | NC_005135.1 | + | 100243 | 1.13 | 0.047598 |
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Target: 5'- aGAACUUCAAAUUCAAGUGUAAGGCAGg -3' miRNA: 3'- -CUUGAAGUUUAAGUUCACAUUCCGUC- -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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