miRNA: 3'- -GG-ACGAGAUA------------UUUC-CGCGUGa--------GGGAC- -5'
miRNA: 3'- -GGACgAgauaUUUCCGCG---UGAGGGAC- -5'
miRNA: 3'- -GGACG------AGAuauUUCCgCGUGAGGGac -5'
miRNA: 3'- ggaCGAGauauuuCCGCGUGAGGGAc -5'
miRNA: 3'- -GGACGAGAUAUUUCCGCGUGAGGGAC- -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 | |||||||
| 28410 | 5' | -52.4 | NC_005946.1 | + | 81561 | 0.66 | 0.935475 |
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Target: 5'- aCCgUGCUCUGUcugcggcugcacAGAGuGCGCAUacugcaaggCCCUGa -3' miRNA: 3'- -GG-ACGAGAUA------------UUUC-CGCGUGa--------GGGAC- -5' |
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| 28410 | 5' | -52.4 | NC_005946.1 | + | 71768 | 0.67 | 0.918688 |
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Target: 5'- uCCUGgUggg-GAAGGUGUcucACUCCCUGg -3' miRNA: 3'- -GGACgAgauaUUUCCGCG---UGAGGGAC- -5' |
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| 28410 | 5' | -52.4 | NC_005946.1 | + | 72775 | 0.67 | 0.906168 |
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Target: 5'- gCCUGCcgggcuUCUuu-GAGG-GCGCUCCCg- -3' miRNA: 3'- -GGACG------AGAuauUUCCgCGUGAGGGac -5' |
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| 28410 | 5' | -52.4 | NC_005946.1 | + | 27693 | 0.68 | 0.892601 |
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Target: 5'- --aGCUC------GGCGCACUCCCUc -3' miRNA: 3'- ggaCGAGauauuuCCGCGUGAGGGAc -5' |
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| 28410 | 5' | -52.4 | NC_005946.1 | + | 69736 | 1.1 | 0.003371 |
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Target: 5'- cCCUGCUCUAUAAAGGCGCACUCCCUGc -3' miRNA: 3'- -GGACGAGAUAUUUCCGCGUGAGGGAC- -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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