miRNA: 3'- -GGGuGGCUacAGGUAcauGGUUCUCG- -5'
miRNA: 3'- -GGGUGGCUACA-----------GGUACa---UGGUU---------CUCG- -5'
miRNA: 3'- -GGGUGGCua--CagGUA-CAUGGUUCUCG- -5'
miRNA: 3'- -GGGUGGCUACAGGUACAUGGUUCUCG- -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 | |||||||
| 4089 | 3' | -51.2 | NC_001655.1 | + | 6876 | 0.66 | 0.446205 |
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Target: 5'- cCCCuCCGAgaUCCGUc--CCAGGAGUg -3' miRNA: 3'- -GGGuGGCUacAGGUAcauGGUUCUCG- -5' |
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| 4089 | 3' | -51.2 | NC_001655.1 | + | 9119 | 0.66 | 0.401924 |
|
Target: 5'- cCCCGCCGAUGUgaguuuggcgaCCAUGguggAUCAGaaccguuucGGGUg -3' miRNA: 3'- -GGGUGGCUACA-----------GGUACa---UGGUU---------CUCG- -5' |
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| 4089 | 3' | -51.2 | NC_001655.1 | + | 9306 | 0.67 | 0.370602 |
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Target: 5'- gUCCGCUGugcaGagCGUaGUACCAAGGGCu -3' miRNA: 3'- -GGGUGGCua--CagGUA-CAUGGUUCUCG- -5' |
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| 4089 | 3' | -51.2 | NC_001655.1 | + | 5665 | 1.15 | 0.00009 |
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Target: 5'- aCCCACCGAUGUCCAUGUACCAAGAGCu -3' miRNA: 3'- -GGGUGGCUACAGGUACAUGGUUCUCG- -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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