miRNA: 3'- -GUCGGCGAgU----------CUCACGCCCAacaaaa -5'
miRNA: 3'- -GUCGGCG------AGUCUCA---CGCCCAACaaaa -5'
miRNA: 3'- gUCG-GCG---AGUCU------CACGCCCAACAAaa -5'
miRNA: 3'- -GUCGGCGa-GUCUC-ACGCCCAacaaaa -5'
miRNA: 3'- -GUCGGCGAGUCUCACGCCCAACAAAA- -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 | |||||||
| 25263 | 5' | -54.3 | NC_005336.1 | + | 44313 | 0.67 | 0.87631 |
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Target: 5'- gCAGCUGCUgGgcuacggcgcGAGUGCGGGUg----- -3' miRNA: 3'- -GUCGGCGAgU----------CUCACGCCCAacaaaa -5' |
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| 25263 | 5' | -54.3 | NC_005336.1 | + | 12711 | 0.67 | 0.868739 |
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Target: 5'- gCAGUCGCaccgcgUCGGGGUcuaGCGGGUUGc--- -3' miRNA: 3'- -GUCGGCG------AGUCUCA---CGCCCAACaaaa -5' |
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| 25263 | 5' | -54.3 | NC_005336.1 | + | 66986 | 0.69 | 0.809741 |
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Target: 5'- uGGCgCGCccgUCGGGcgugguGUGCGGGUUGUUg- -3' miRNA: 3'- gUCG-GCG---AGUCU------CACGCCCAACAAaa -5' |
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| 25263 | 5' | -54.3 | NC_005336.1 | + | 97309 | 0.7 | 0.742318 |
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Target: 5'- gCGGCCGUggCGGAGcUGCGGGUg----- -3' miRNA: 3'- -GUCGGCGa-GUCUC-ACGCCCAacaaaa -5' |
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| 25263 | 5' | -54.3 | NC_005336.1 | + | 8662 | 1.06 | 0.005028 |
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Target: 5'- gCAGCCGCUCAGAGUGCGGGUUGUUUUg -3' miRNA: 3'- -GUCGGCGAGUCUCACGCCCAACAAAA- -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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