miRNA: 3'- gGGCuCCCaaGGCaCGUCC-GCCUuau -5'
miRNA: 3'- -GGGcuCCCaaGgCACGUCCGCCuuau -5'
miRNA: 3'- gGGCUCCCaAGGCACGUC-CG-----CCUUau -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
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| Predicted miRNA align pattern | |||||||
| 26494 | 3' | -57.2 | NC_005357.1 | + | 41480 | 0.66 | 0.536042 |
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Target: 5'- gCCGuGGGcaCCGcGCAGGaCGGAc-- -3' miRNA: 3'- gGGCuCCCaaGGCaCGUCC-GCCUuau -5' |
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| 26494 | 3' | -57.2 | NC_005357.1 | + | 37066 | 0.68 | 0.395909 |
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Target: 5'- aCCCu-GGGcgCgGUGCAGGCGGc--- -3' miRNA: 3'- -GGGcuCCCaaGgCACGUCCGCCuuau -5' |
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| 26494 | 3' | -57.2 | NC_005357.1 | + | 16992 | 0.72 | 0.254207 |
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Target: 5'- aCCGAGGGcUUCGUGCAGcGCaugacGGAAa- -3' miRNA: 3'- gGGCUCCCaAGGCACGUC-CG-----CCUUau -5' |
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| 26494 | 3' | -57.2 | NC_005357.1 | + | 24614 | 1.08 | 0.000562 |
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Target: 5'- gCCCGAGGGUUCCGUGCAGGCGGAAUAc -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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