miRNA: 3'- -UAGCUCGAgaaacCCCAGCUGUAAUU- -5'
miRNA: 3'- -UAGCUCGagaaaCCCCAGCUGUAAuu -5'
miRNA: 3'- uagCUCGAGa---A---------------ACCCCAGCUGUAAUU- -5'
miRNA: 3'- -UAGCUCGAGAAACCCCAGCUGUAAUU- -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 | |||||||
| 8736 | 5' | -50.6 | NC_002331.1 | + | 20384 | 0.67 | 0.987872 |
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Target: 5'- uAUCGAGUUa----GGGUCGAUAUUAAu -3' miRNA: 3'- -UAGCUCGAgaaacCCCAGCUGUAAUU- -5' |
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| 8736 | 5' | -50.6 | NC_002331.1 | + | 85404 | 0.67 | 0.982448 |
|
Target: 5'- cAUUGAGCgauaaGGGGUUGACAUUu- -3' miRNA: 3'- -UAGCUCGagaaaCCCCAGCUGUAAuu -5' |
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| 8736 | 5' | -50.6 | NC_002331.1 | + | 111654 | 0.73 | 0.8182 |
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Target: 5'- --aGAGCUCgauuUaaaaacucugggacuUGGGGUCGACAUUAAa -3' miRNA: 3'- uagCUCGAGa---A---------------ACCCCAGCUGUAAUU- -5' |
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| 8736 | 5' | -50.6 | NC_002331.1 | + | 111466 | 1.05 | 0.016651 |
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Target: 5'- aAUCGAGCUCUUUGGGGUCGACAUUAAa -3' miRNA: 3'- -UAGCUCGAGAAACCCCAGCUGUAAUU- -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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