miRNA: 3'- ccuAAGA----GGCCAGaCUGGUAGCCAcc -5'
miRNA: 3'- -CCUaAGAGGCC-------------AGaCUGgUAGCCAC-C- -5'
miRNA: 3'- -CCUaag-AGGCCAGACUgguaGCCACC- -5'
miRNA: 3'- cCUAAGA-GGCCAGACUGGUa--GCCacc -5'
miRNA: 3'- -CCUAAGAGGCCAGACUGGUAGCCACC- -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 | |||||||
| 13165 | 5' | -52.9 | NC_003401.1 | + | 96724 | 0.66 | 0.980636 |
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Target: 5'- --uUUCUugcgCCGGUCgGGCCGUUGGUu- -3' miRNA: 3'- ccuAAGA----GGCCAGaCUGGUAGCCAcc -5' |
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| 13165 | 5' | -52.9 | NC_003401.1 | + | 82564 | 0.66 | 0.98042 |
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Target: 5'- uGGAaUCUCCGGaaccagugccugcUC-GGCgAUCGGUGcGg -3' miRNA: 3'- -CCUaAGAGGCC-------------AGaCUGgUAGCCAC-C- -5' |
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| 13165 | 5' | -52.9 | NC_003401.1 | + | 89591 | 0.68 | 0.930142 |
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Target: 5'- uGGAgugaUCUGGUCUGGaug-CGGUGGu -3' miRNA: 3'- -CCUaag-AGGCCAGACUgguaGCCACC- -5' |
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| 13165 | 5' | -52.9 | NC_003401.1 | + | 73465 | 0.71 | 0.850345 |
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Target: 5'- aGGUUCUcCCGGUUUGACCAcgaCGGg-- -3' miRNA: 3'- cCUAAGA-GGCCAGACUGGUa--GCCacc -5' |
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| 13165 | 5' | -52.9 | NC_003401.1 | + | 125763 | 1.13 | 0.003215 |
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Target: 5'- gGGAUUCUCCGGUCUGACCAUCGGUGGa -3' miRNA: 3'- -CCUAAGAGGCCAGACUGGUAGCCACC- -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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