miRNA: 3'- gcaAGACGGUGGg------CAgCGUGCCCUau -5'
miRNA: 3'- gcaAGACGGUGGGCAGCG--------UGCCCuaU- -5'
miRNA: 3'- -GCAAGA----------CGGUGGGCAGCGU-GCCCuau -5'
miRNA: 3'- -GCAAGACGGUGGGCaGCGUGcccuau -5'
miRNA: 3'- -GCAAGACGGUGGGCAGCGUGCCCUAU- -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 | |||||||
| 22889 | 5' | -57.4 | NC_005137.2 | + | 106507 | 0.67 | 0.743952 |
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Target: 5'- --aUUUGCCACUaccaagaGUgGCACGGGAa- -3' miRNA: 3'- gcaAGACGGUGGg------CAgCGUGCCCUau -5' |
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| 22889 | 5' | -57.4 | NC_005137.2 | + | 88470 | 0.68 | 0.714413 |
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Target: 5'- --aUUUGCCACCUGUUGCcgauucggGCGGGcgAg -3' miRNA: 3'- gcaAGACGGUGGGCAGCG--------UGCCCuaU- -5' |
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| 22889 | 5' | -57.4 | NC_005137.2 | + | 74406 | 0.69 | 0.633206 |
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Target: 5'- aCGUUUUuaucgagcacGUCGCCCGUCGCGuCGGGu-- -3' miRNA: 3'- -GCAAGA----------CGGUGGGCAGCGU-GCCCuau -5' |
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| 22889 | 5' | -57.4 | NC_005137.2 | + | 95590 | 0.7 | 0.582139 |
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Target: 5'- cCGUUUUGCCGCCCG-CGCACu----- -3' miRNA: 3'- -GCAAGACGGUGGGCaGCGUGcccuau -5' |
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| 22889 | 5' | -57.4 | NC_005137.2 | + | 52308 | 1.06 | 0.00266 |
|
Target: 5'- cCGUUCUGCCACCCGUCGCACGGGAUAc -3' miRNA: 3'- -GCAAGACGGUGGGCAGCGUGCCCUAU- -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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