miRNA: 3'- -UC-GUGUagUCGUa---GGCGCUGGCCGac -5'
miRNA: 3'- uCGUG--UAGUCGUAGGC-------GCUGGCCgac -5'
miRNA: 3'- -UCGUGUaGUCGuAG-GCGcUGGCCGAc -5'
miRNA: 3'- -UCGUGUAGUCGUAGGCGCUGGCCGAC- -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 | |||||||
| 3488 | 3' | -57.6 | NC_001609.1 | + | 6735 | 0.66 | 0.194016 |
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Target: 5'- cGGcCGCAaaGGUGgcugCCGUGACCGGCa- -3' miRNA: 3'- -UC-GUGUagUCGUa---GGCGCUGGCCGac -5' |
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| 3488 | 3' | -57.6 | NC_001609.1 | + | 6517 | 0.66 | 0.193436 |
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Target: 5'- uGUGCcgGUCAGCAUCCGgcauuccCGGCCGGg-- -3' miRNA: 3'- uCGUG--UAGUCGUAGGC-------GCUGGCCgac -5' |
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| 3488 | 3' | -57.6 | NC_001609.1 | + | 6486 | 0.68 | 0.122507 |
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Target: 5'- cGGCGCGcCAGC-UCaCGCcACCGGCUc -3' miRNA: 3'- -UCGUGUaGUCGuAG-GCGcUGGCCGAc -5' |
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| 3488 | 3' | -57.6 | NC_001609.1 | + | 11105 | 1.08 | 0.000058 |
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Target: 5'- cAGCACAUCAGCAUCCGCGACCGGCUGa -3' miRNA: 3'- -UCGUGUAGUCGUAGGCGCUGGCCGAC- -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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