miRNA: 3'- uUGCGUUGGU----------GCUUCAGGCGacucuu -5'
miRNA: 3'- uUGCGUUGGuGCUUCaGGCGa--------CUCUU- -5'
miRNA: 3'- uuGCGuUGGUGCUUCAGGCGACu--CUu -5'
miRNA: 3'- -UUGCGUUGGUGCUUCAGGCGACUCUU- -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 | |||||||
| 27570 | 3' | -53.9 | NC_005882.1 | + | 26683 | 0.68 | 0.514634 |
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Target: 5'- cGCGCGGCCAaccgugauccCGAGGUCCGCa----- -3' miRNA: 3'- uUGCGUUGGU----------GCUUCAGGCGacucuu -5' |
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| 27570 | 3' | -53.9 | NC_005882.1 | + | 4183 | 0.69 | 0.460252 |
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Target: 5'- uGCGCGACCuCGAAGaCCGCgugaugcgcGAGAGu -3' miRNA: 3'- uUGCGUUGGuGCUUCaGGCGa--------CUCUU- -5' |
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| 27570 | 3' | -53.9 | NC_005882.1 | + | 3460 | 0.73 | 0.263966 |
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Target: 5'- -cCGC-ACCGCGAAGUCUGCUGccuGAc -3' miRNA: 3'- uuGCGuUGGUGCUUCAGGCGACu--CUu -5' |
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| 27570 | 3' | -53.9 | NC_005882.1 | + | 7994 | 1.04 | 0.00138 |
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Target: 5'- gAACGCAACCACGAAGUCCGCUGAGAAg -3' miRNA: 3'- -UUGCGUUGGUGCUUCAGGCGACUCUU- -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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