miRNA: 3'- -GGGCUCCCAAGGCACGUCCGCCUUAU- -5'
miRNA: 3'- gGGCUCCCaAGGCACGUC-CG-----CCUUau -5'
miRNA: 3'- gGGCuCCCaaGGCaCGUCC-GCCUuau -5'
miRNA: 3'- -GGGcuCCCaaGgCACGUCCGCCuuau -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 |
| Predicted miRNA align pattern | |||||||
| 26684 | 3' | -57.2 | NC_005808.1 | + | 24784 | 1.08 | 0.000565 |
|
Target: 5'- gCCCGAGGGUUCCGUGCAGGCGGAAUAc -3' miRNA: 3'- -GGGCUCCCAAGGCACGUCCGCCUUAU- -5' |
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| 26684 | 3' | -57.2 | NC_005808.1 | + | 17162 | 0.72 | 0.254986 |
|
Target: 5'- aCCGAGGGcUUCGUGCAGcGCaugacGGAAa- -3' miRNA: 3'- gGGCUCCCaAGGCACGUC-CG-----CCUUau -5' |
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| 26684 | 3' | -57.2 | NC_005808.1 | + | 41650 | 0.66 | 0.537212 |
|
Target: 5'- gCCGuGGGcaCCGcGCAGGaCGGAc-- -3' miRNA: 3'- gGGCuCCCaaGGCaCGUCC-GCCUuau -5' |
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| 26684 | 3' | -57.2 | NC_005808.1 | + | 37236 | 0.68 | 0.396946 |
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Target: 5'- aCCCu-GGGcgCgGUGCAGGCGGc--- -3' miRNA: 3'- -GGGcuCCCaaGgCACGUCCGCCuuau -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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