miRNA: 3'- -CGGGCCUGg---GAgUCACU-------AGUCCugUU- -5'
miRNA: 3'- cGGGCC-----UGGGAGUCa-CUA----GUCCUGuu -5'
miRNA: 3'- cGGGCCUGGGAgUCaCUaGUCCUguu -5'
miRNA: 3'- -CGGGCCUGGGAGUCACUAGUCCUGUU- -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 | |||||||
| 8122 | 5' | -57 | NC_001978.2 | + | 16747 | 0.66 | 0.533406 |
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Target: 5'- aGCCUGGGCgcuaCUgGGUGAcguggcuUCAGGugAAu -3' miRNA: 3'- -CGGGCCUGg---GAgUCACU-------AGUCCugUU- -5' |
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| 8122 | 5' | -57 | NC_001978.2 | + | 38256 | 0.66 | 0.523698 |
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Target: 5'- cCCCGGcggcaACCCUCAGcgGAUgcccCGGGGCu- -3' miRNA: 3'- cGGGCC-----UGGGAGUCa-CUA----GUCCUGuu -5' |
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| 8122 | 5' | -57 | NC_001978.2 | + | 16033 | 0.66 | 0.502375 |
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Target: 5'- uUCCGGACCCUgGG-GAcCGGGAa-- -3' miRNA: 3'- cGGGCCUGGGAgUCaCUaGUCCUguu -5' |
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| 8122 | 5' | -57 | NC_001978.2 | + | 25761 | 1.08 | 0.000515 |
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Target: 5'- cGCCCGGACCCUCAGUGAUCAGGACAAc -3' miRNA: 3'- -CGGGCCUGGGAGUCACUAGUCCUGUU- -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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