miRNA: 3'- cGGUUCCGCaGaGGCUCGc-GGCCGCu -5'
miRNA: 3'- -CGGuUCCG---CAGAGgCuCGCGGCCGCU- -5'
miRNA: 3'- -CGGUUCCGCAGAG---GCuCGcGGCC-GCU- -5'
miRNA: 3'- -CGGuuCCGC--AG-AGGCUCGCGGCCgcu -5'
miRNA: 3'- cGGUUC-CGCAGaGGC-----UCGCG-GcCGCU- -5'
Results 21 - 25 of 25 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 | |||||||
| 30856 | 3' | -61.1 | NC_006552.1 | + | 17951 | 0.69 | 0.326799 |
|
Target: 5'- cCCGAGGCG-CgCCGAGUuaCCGGCGu -3' miRNA: 3'- cGGUUCCGCaGaGGCUCGc-GGCCGCu -5' |
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| 30856 | 3' | -61.1 | NC_006552.1 | + | 61373 | 0.68 | 0.342149 |
|
Target: 5'- aGCC-GGGCcauGUUUUgGcGCGCCGGCGGc -3' miRNA: 3'- -CGGuUCCG---CAGAGgCuCGCGGCCGCU- -5' |
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| 30856 | 3' | -61.1 | NC_006552.1 | + | 37969 | 0.68 | 0.350016 |
|
Target: 5'- gGCCAGGGCGUCUUgcaCG-GC-CUGGuCGAu -3' miRNA: 3'- -CGGUUCCGCAGAG---GCuCGcGGCC-GCU- -5' |
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| 30856 | 3' | -61.1 | NC_006552.1 | + | 54121 | 0.68 | 0.366135 |
|
Target: 5'- gGCUcuGGCGcaUCgUCUGAGCGCCGGg-- -3' miRNA: 3'- -CGGuuCCGC--AG-AGGCUCGCGGCCgcu -5' |
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| 30856 | 3' | -61.1 | NC_006552.1 | + | 7194 | 0.66 | 0.492274 |
|
Target: 5'- cCCAAGcGCGUC-CCGuccccGGCGCgCaGCGAg -3' miRNA: 3'- cGGUUC-CGCAGaGGC-----UCGCG-GcCGCU- -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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