miRNA: 3'- gCGUCGACCCUG-GUCgGGCuCGGGGU- -5'
miRNA: 3'- gCGUCGACCcUGG-------------UCGGGCUCG-----GGGU- -5'
miRNA: 3'- -GCgUCGACCCUGGUCG-GGCUCGGggu -5'
miRNA: 3'- -GCGUCGACCCUGGUCGGGCUCGGGGU- -5'
Results 1 - 4 of 4 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 | |||||||
| 32874 | 5' | -64.4 | NC_007408.1 | + | 1636 | 0.66 | 0.036896 |
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Target: 5'- uGUGGUUGGGGCuCGGgCUG-GUCCCAg -3' miRNA: 3'- gCGUCGACCCUG-GUCgGGCuCGGGGU- -5' |
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| 32874 | 5' | -64.4 | NC_007408.1 | + | 6498 | 0.69 | 0.020377 |
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Target: 5'- uGCGGCUGG-ACUgaacgucagcauaGGCCCGAGCuaaauCCCAc -3' miRNA: 3'- gCGUCGACCcUGG-------------UCGGGCUCG-----GGGU- -5' |
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| 32874 | 5' | -64.4 | NC_007408.1 | + | 3554 | 0.69 | 0.01914 |
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Target: 5'- uCGgGGCUGGGACCGGCgUUGGGCUg-- -3' miRNA: 3'- -GCgUCGACCCUGGUCG-GGCUCGGggu -5' |
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| 32874 | 5' | -64.4 | NC_007408.1 | + | 1598 | 1.08 | 5e-06 |
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Target: 5'- cCGCAGCUGGGACCAGCCCGAGCCCCAa -3' miRNA: 3'- -GCGUCGACCCUGGUCGGGCUCGGGGU- -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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