miRNA: 3'- acuuaCAuUGUCCUCGUCCga-GGUuu -5'
miRNA: 3'- -ACUU--ACAuUGUCCUCGUC----------CGAGGuuu -5'
miRNA: 3'- -ACuuACAUUGUCCu------CGUCCGa----------GGUUU- -5'
miRNA: 3'- acUUACauUGUCC-UCGU--CCGAGGUUU- -5'
miRNA: 3'- -ACUUACAUUGUCCUCGUCCGAGGUUU- -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 | |||||||
| 28199 | 5' | -50.4 | NC_005891.1 | + | 14793 | 0.66 | 0.824271 |
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Target: 5'- ----cGUuGCAGGAGCAGGaagCCGu- -3' miRNA: 3'- acuuaCAuUGUCCUCGUCCga-GGUuu -5' |
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| 28199 | 5' | -50.4 | NC_005891.1 | + | 12463 | 0.67 | 0.793411 |
|
Target: 5'- uUGGAcuUGUuGCGGGAGCAGaaaauaacuuGCUCCu-- -3' miRNA: 3'- -ACUU--ACAuUGUCCUCGUC----------CGAGGuuu -5' |
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| 28199 | 5' | -50.4 | NC_005891.1 | + | 16232 | 0.68 | 0.703423 |
|
Target: 5'- cUGggUGUGGCAGGuaguuuuGCAGGUgcguucgcuucCCAAAc -3' miRNA: 3'- -ACuuACAUUGUCCu------CGUCCGa----------GGUUU- -5' |
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| 28199 | 5' | -50.4 | NC_005891.1 | + | 11482 | 0.71 | 0.525683 |
|
Target: 5'- -uGGUGgcGCAGGcGGCAacGGCUCCGGAg -3' miRNA: 3'- acUUACauUGUCC-UCGU--CCGAGGUUU- -5' |
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| 28199 | 5' | -50.4 | NC_005891.1 | + | 10594 | 1.07 | 0.002057 |
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Target: 5'- gUGAAUGUAACAGGAGCAGGCUCCAAAg -3' miRNA: 3'- -ACUUACAUUGUCCUCGUCCGAGGUUU- -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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