miRNA: 3'- cuUUCUCGU-Ga-----CCGAUUGGuCCGAgC- -5'
miRNA: 3'- -CUUUCUCGUGACCgaUUG-------------GUCCG--AGc -5'
miRNA: 3'- cuuucUC-GUGaCCGAUUGGUCCGAGC- -5'
miRNA: 3'- cuuuCUCGuGACCGAUUGGUC-CGAGc -5'
miRNA: 3'- -CUUUCUCGUGACCGAUUGGUCCGAGC- -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 | |||||||
| 2363 | 3' | -52.9 | NC_001416.1 | + | 3733 | 0.66 | 0.786831 |
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Target: 5'- -cAGGAGCAgCgggaaaGGCUGACC-GGCUgGa -3' miRNA: 3'- cuUUCUCGU-Ga-----CCGAUUGGuCCGAgC- -5' |
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| 2363 | 3' | -52.9 | NC_001416.1 | + | 850 | 0.66 | 0.764911 |
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Target: 5'- aGGAAGGGCGCUGGgaAACacugcccuuucagCGGGCcaUCa -3' miRNA: 3'- -CUUUCUCGUGACCgaUUG-------------GUCCG--AGc -5' |
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| 2363 | 3' | -52.9 | NC_001416.1 | + | 39768 | 0.7 | 0.541085 |
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Target: 5'- ----uGGuCAC-GGUUAGCCAGGCUCGc -3' miRNA: 3'- cuuucUC-GUGaCCGAUUGGUCCGAGC- -5' |
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| 2363 | 3' | -52.9 | NC_001416.1 | + | 44786 | 0.76 | 0.256609 |
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Target: 5'- ---cGAGC-CUGGUUAGCCAGuGCUCu -3' miRNA: 3'- cuuuCUCGuGACCGAUUGGUC-CGAGc -5' |
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| 2363 | 3' | -52.9 | NC_001416.1 | + | 44859 | 1.08 | 0.00144 |
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Target: 5'- gGAAAGAGCACUGGCUAACCAGGCUCGc -3' miRNA: 3'- -CUUUCUCGUGACCGAUUGGUCCGAGC- -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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