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miRNA: 3'- cAGAGGCUCUUGGA----CGA----------CUGUC----AGCG- -5'
miRNA: 3'- -CAGa-GGCUCUUGGA---------------CGa-CUGUCaGCG- -5'
miRNA: 3'- caGAGG--CUCUUGGACGAC-UGuCaGCG- -5'
miRNA: 3'- caGAGGCUCUUGGaCGA--CUGUCa--GCG- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 28933 | 3' | -53.9 | NC_006146.1 | + | 45949 | 0.66 | 0.973686 |
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Target: 5'- cUCUCUGGGGACCUcgacGCUcucugcccggGGCAGcuccUCGCc -3' miRNA: 3'- cAGAGGCUCUUGGA----CGA----------CUGUC----AGCG- -5' |
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| 28933 | 3' | -53.9 | NC_006146.1 | + | 106421 | 0.66 | 0.972043 |
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Target: 5'- gGUUggCCGAGAACCUcagaaaugcccuucaGCagGACAG-CGCc -3' miRNA: 3'- -CAGa-GGCUCUUGGA---------------CGa-CUGUCaGCG- -5' |
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| 28933 | 3' | -53.9 | NC_006146.1 | + | 120845 | 0.66 | 0.967923 |
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Target: 5'- -cUUCCugGAGGGCCUGCUGgACuG-CGCc -3' miRNA: 3'- caGAGG--CUCUUGGACGAC-UGuCaGCG- -5' |
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| 28933 | 3' | -53.9 | NC_006146.1 | + | 41058 | 0.66 | 0.964728 |
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Target: 5'- -cUUCCGAGGGCUcGCUcgGACGGgggCGUg -3' miRNA: 3'- caGAGGCUCUUGGaCGA--CUGUCa--GCG- -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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