miRNA: 3'- gaAGCAAGCUGa-----CUUAUAGu-CUC----UGU- -5'
miRNA: 3'- gaAGCaAGCu-GACUUAU---AGUCUCUGU- -5'
miRNA: 3'- gAAGCaAGCUGACUuaUAGUC-UCUGu -5'
miRNA: 3'- -GAAGCa----AGCUGACUuauaGUCUCUGu -5'
miRNA: 3'- -GAAGCAAGCUGACUUAUAGUCUCUGU- -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 | |||||||
| 12639 | 3' | -45 | NC_003345.1 | + | 46651 | 0.66 | 0.999812 |
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Target: 5'- -cUCGUUCGACguugagGAGUAUCccGAGuuccGCAu -3' miRNA: 3'- gaAGCAAGCUGa-----CUUAUAGu-CUC----UGU- -5' |
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| 12639 | 3' | -45 | NC_003345.1 | + | 45831 | 0.67 | 0.999483 |
|
Target: 5'- -gUCG-UCGccCUGAAUGuccUCGGAGACGu -3' miRNA: 3'- gaAGCaAGCu-GACUUAU---AGUCUCUGU- -5' |
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| 12639 | 3' | -45 | NC_003345.1 | + | 45285 | 0.67 | 0.999347 |
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Target: 5'- aUUCGaUUGGCUGA--GUCAGaAGACc -3' miRNA: 3'- gAAGCaAGCUGACUuaUAGUC-UCUGu -5' |
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| 12639 | 3' | -45 | NC_003345.1 | + | 6986 | 0.72 | 0.974689 |
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Target: 5'- uCUUCGgcuggUCGGCUGA----CAGAGACu -3' miRNA: 3'- -GAAGCa----AGCUGACUuauaGUCUCUGu -5' |
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| 12639 | 3' | -45 | NC_003345.1 | + | 51457 | 1.11 | 0.015023 |
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Target: 5'- uCUUCGUUCGACUGAAUAUCAGAGACAa -3' miRNA: 3'- -GAAGCAAGCUGACUUAUAGUCUCUGU- -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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