miRNA: 3'- gguaGCGGa----UACGGGCGCU------------CCGUuau -5'
miRNA: 3'- -GGUa--GCGgauACGGGCGCuCCGUUAu -5'
miRNA: 3'- -GGuaGCGGAUACGGGCGCUCCGUUau -5'
miRNA: 3'- -GGUAGCGGAUACGGGCGCUCCGUUAu -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 | |||||||
| 16941 | 3' | -55.3 | NC_004313.1 | + | 15059 | 0.66 | 0.625245 |
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Target: 5'- ---aCGCCgcaggAUGCCCGCGAauacaugcagcaGGCGc-- -3' miRNA: 3'- gguaGCGGa----UACGGGCGCU------------CCGUuau -5' |
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| 16941 | 3' | -55.3 | NC_004313.1 | + | 33290 | 0.67 | 0.535448 |
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Target: 5'- aCCAgagCGC---UGCCUGCGuGGCGAUc -3' miRNA: 3'- -GGUa--GCGgauACGGGCGCuCCGUUAu -5' |
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| 16941 | 3' | -55.3 | NC_004313.1 | + | 2744 | 0.77 | 0.120073 |
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Target: 5'- aCC--UGUCUGUGCCUGCGGGGCAAc- -3' miRNA: 3'- -GGuaGCGGAUACGGGCGCUCCGUUau -5' |
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| 16941 | 3' | -55.3 | NC_004313.1 | + | 2969 | 1.06 | 0.001035 |
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Target: 5'- cCCAUCGCCUAUGCCCGCGAGGCAAUu -3' miRNA: 3'- -GGUAGCGGAUACGGGCGCUCCGUUAu -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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