miRNA: 3'- -AGAa-GGCG----AAGAGGAGCCUGUAGguu -5'
miRNA: 3'- -AGAAGGCGaa------------GAGGAGCCUGUa--GGUu -5'
miRNA: 3'- agaaGGCGa--AGAGGAGC--CUGUAGGUu -5'
miRNA: 3'- -AGAAGGCGAAGAGGAGCCUGUAGGUU- -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 | |||||||
| 28911 | 3' | -53.8 | NC_006146.1 | + | 84500 | 0.67 | 0.947933 |
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Target: 5'- uUCUggCUGUggugUUUUCCUCGGACGUCg-- -3' miRNA: 3'- -AGAa-GGCG----AAGAGGAGCCUGUAGguu -5' |
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| 28911 | 3' | -53.8 | NC_006146.1 | + | 15134 | 0.7 | 0.822921 |
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Target: 5'- cUCUUCUGCggcggggucuacagCUCCUCGGGCGacgCCGu -3' miRNA: 3'- -AGAAGGCGaa------------GAGGAGCCUGUa--GGUu -5' |
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| 28911 | 3' | -53.8 | NC_006146.1 | + | 56605 | 0.71 | 0.804322 |
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Target: 5'- ---gCCGCcggUCUCCUCGccGGCGUCCAu -3' miRNA: 3'- agaaGGCGa--AGAGGAGC--CUGUAGGUu -5' |
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| 28911 | 3' | -53.8 | NC_006146.1 | + | 16328 | 1.06 | 0.006908 |
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Target: 5'- cUCUUCCGCUUCUCCUCGGACAUCCAAu -3' miRNA: 3'- -AGAAGGCGAAGAGGAGCCUGUAGGUU- -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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