miRNA: 3'- caGAGGCuCUUGGa----CGa-CUGUCAGCg -5'
miRNA: 3'- caGAGGCUCUUGGaCGA--CUGUCa--GCG- -5'
miRNA: 3'- -CAGAGG-----CUCUUGGACG------AC--UGUC-AGCG- -5'
miRNA: 3'- -CAGAGGcUCUUGGACGACUGUCAGCG- -5'
Results 21 - 24 of 24 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 | |||||||
| 28933 | 3' | -53.9 | NC_006146.1 | + | 43915 | 0.66 | 0.973686 |
|
Target: 5'- -gCUCCG-GGACCgcgucGCccGGCAGUCGg -3' miRNA: 3'- caGAGGCuCUUGGa----CGa-CUGUCAGCg -5' |
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| 28933 | 3' | -53.9 | NC_006146.1 | + | 41058 | 0.66 | 0.964728 |
|
Target: 5'- -cUUCCGAGGGCUcGCUcgGACGGgggCGUg -3' miRNA: 3'- caGAGGCUCUUGGaCGA--CUGUCa--GCG- -5' |
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| 28933 | 3' | -53.9 | NC_006146.1 | + | 40075 | 0.7 | 0.844036 |
|
Target: 5'- cGUCUCCcggcgGAGGGCCUGCagcgcgUGcuGCAGcUCGCu -3' miRNA: 3'- -CAGAGG-----CUCUUGGACG------AC--UGUC-AGCG- -5' |
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| 28933 | 3' | -53.9 | NC_006146.1 | + | 1990 | 1.01 | 0.017673 |
|
Target: 5'- cGUCUCC-AGAACCUGCUGACAGUCGCg -3' miRNA: 3'- -CAGAGGcUCUUGGACGACUGUCAGCG- -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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