miRNA: 3'- -GGGCGuGGCaCCGGC--------------UAGG-CCAGUUc -5'
miRNA: 3'- -GGGCGuGGcaCCGGCUAG-GCCAGUUC- -5'
miRNA: 3'- -GGGCGUGGCACCGGCUAGGCCAGUUC- -5'
Results 1 - 3 of 3 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 | |||||||
| 1321 | 3' | -58.7 | NC_001331.1 | + | 657 | 0.66 | 0.113435 |
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Target: 5'- uUCCGC-CCGaGGCCGcuggauacguggacAUCCuGGUCAAc -3' miRNA: 3'- -GGGCGuGGCaCCGGC--------------UAGG-CCAGUUc -5' |
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| 1321 | 3' | -58.7 | NC_001331.1 | + | 1932 | 0.69 | 0.064225 |
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Target: 5'- gCCCGC-CC--GGCUGGUCgUGGUCGGGg -3' miRNA: 3'- -GGGCGuGGcaCCGGCUAG-GCCAGUUC- -5' |
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| 1321 | 3' | -58.7 | NC_001331.1 | + | 6860 | 1.11 | 1.9e-05 |
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Target: 5'- gCCCGCACCGUGGCCGAUCCGGUCAAGg -3' miRNA: 3'- -GGGCGUGGCACCGGCUAGGCCAGUUC- -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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