miRNA: 3'- -GACU---ACACGUc---GCGGGGuCGGGACag -5'
miRNA: 3'- gaCUACACGUCGCGGGGU--------CGGgACAG- -5'
miRNA: 3'- gaCUACa-CGUC-GCGGGGUCGGGA-CAG- -5'
miRNA: 3'- -GACUACACGUCGCGGGGUCGGGACAG- -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 | |||||||
| 13015 | 5' | -59.8 | NC_003390.1 | + | 5878 | 0.66 | 0.408524 |
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Target: 5'- uCUGAgcgUGUGCAagccCGCCCC-GUCCUGg- -3' miRNA: 3'- -GACU---ACACGUc---GCGGGGuCGGGACag -5' |
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| 13015 | 5' | -59.8 | NC_003390.1 | + | 31104 | 0.69 | 0.25768 |
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Target: 5'- -cGAUGUGCGGUGUCUCAacguugugGCUgUGUCu -3' miRNA: 3'- gaCUACACGUCGCGGGGU--------CGGgACAG- -5' |
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| 13015 | 5' | -59.8 | NC_003390.1 | + | 2793 | 0.77 | 0.063032 |
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Target: 5'- -cGGUGagGUAGcCGCCCCGGCCCUcGUCu -3' miRNA: 3'- gaCUACa-CGUC-GCGGGGUCGGGA-CAG- -5' |
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| 13015 | 5' | -59.8 | NC_003390.1 | + | 6786 | 1.09 | 0.000254 |
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Target: 5'- gCUGAUGUGCAGCGCCCCAGCCCUGUCu -3' miRNA: 3'- -GACUACACGUCGCGGGGUCGGGACAG- -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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