miRNA: 3'- -GUUAUGGCUAaAGGA---UCUACgg-----GGAG- -5'
miRNA: 3'- gUUAUGGCUaaa-------GGAUCuaCGGGGag -5'
miRNA: 3'- guuAUGGCua-AAGGAUCUACGGgGAg -5'
miRNA: 3'- -GUUAUG-GCUAa---AgGA---UCUACGGGGAG- -5'
miRNA: 3'- -GUUAUGGCUAAAGGAUCUACGGGGAG- -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 | |||||||
| 30734 | 3' | -49.4 | NC_006552.1 | + | 31326 | 0.66 | 0.9655 |
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Target: 5'- uCGGUACCGGUgUCCUuguAGAUGaugauugCCUCg -3' miRNA: 3'- -GUUAUGGCUAaAGGA---UCUACgg-----GGAG- -5' |
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| 30734 | 3' | -49.4 | NC_006552.1 | + | 29035 | 0.68 | 0.907119 |
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Target: 5'- gAAUGCCGAggaaucccagCCUGGcgGCUCCa- -3' miRNA: 3'- gUUAUGGCUaaa-------GGAUCuaCGGGGag -5' |
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| 30734 | 3' | -49.4 | NC_006552.1 | + | 38449 | 0.7 | 0.845027 |
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Target: 5'- --cUGCUGcugUUCCUGGAUGCCgCUg -3' miRNA: 3'- guuAUGGCua-AAGGAUCUACGGgGAg -5' |
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| 30734 | 3' | -49.4 | NC_006552.1 | + | 43652 | 0.71 | 0.787134 |
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Target: 5'- gUAGUGCuCGAUcaggUgCUggcAGAUGCCCCUCc -3' miRNA: 3'- -GUUAUG-GCUAa---AgGA---UCUACGGGGAG- -5' |
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| 30734 | 3' | -49.4 | NC_006552.1 | + | 47733 | 1.11 | 0.003268 |
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Target: 5'- gCAAUACCGAUUUCCUAGAUGCCCCUCg -3' miRNA: 3'- -GUUAUGGCUAAAGGAUCUACGGGGAG- -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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