miRNA: 3'- -ACGACGU-AG---------------UCGAUG----CGCCaGUUCAA- -5'
miRNA: 3'- aCGACGUa-----GUCGA--UGCGCCAgu-UCaa -5'
miRNA: 3'- aCGACGUAGUCGaUgCGCCag-UUCAa -5'
miRNA: 3'- acgACGUAGUCgaUGCGCCaGUUCAA- -5'
miRNA: 3'- -ACGACGUAGUCGAUGCGCCAGUUCAA- -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 | |||||||
| 8426 | 3' | -53.5 | NC_002166.1 | + | 20239 | 0.66 | 0.672818 |
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Target: 5'- aUGCUGCAgUCacgcaauaauuaacgGGCUGCggcaGCGGcCAGGUUg -3' miRNA: 3'- -ACGACGU-AG---------------UCGAUG----CGCCaGUUCAA- -5' |
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| 8426 | 3' | -53.5 | NC_002166.1 | + | 16558 | 0.66 | 0.668175 |
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Target: 5'- cGCUGCGgucaacCAGCUgcGCGCGGUaccAGa- -3' miRNA: 3'- aCGACGUa-----GUCGA--UGCGCCAgu-UCaa -5' |
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| 8426 | 3' | -53.5 | NC_002166.1 | + | 27314 | 0.68 | 0.552116 |
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Target: 5'- aGCUGUGUCAGC-AgGCGGgcaAAGUc -3' miRNA: 3'- aCGACGUAGUCGaUgCGCCag-UUCAa -5' |
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| 8426 | 3' | -53.5 | NC_002166.1 | + | 28298 | 0.69 | 0.474416 |
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Target: 5'- --aUGCGUCGGgaGCGCGG-CGGGUUc -3' miRNA: 3'- acgACGUAGUCgaUGCGCCaGUUCAA- -5' |
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| 8426 | 3' | -53.5 | NC_002166.1 | + | 15719 | 1.05 | 0.001408 |
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Target: 5'- gUGCUGCAUCAGCUACGCGGUCAAGUUu -3' miRNA: 3'- -ACGACGUAGUCGAUGCGCCAGUUCAA- -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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