miRNA: 3'- gaauAGAGCA----GGACACG----------GUGGUCGUu -5'
miRNA: 3'- gAAUAG----AGCAGGAC---ACGGUGGUCGUu -5'
miRNA: 3'- gaauAGAGCA---GGACACGGUGGUCGuu -5'
miRNA: 3'- gaaUAGAGCaGG---ACACGGUGGUCGUU- -5'
miRNA: 3'- -GAAUAGAGCAGGACACGGUGGUCGUU- -5'
Results 1 - 5 of 5 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 | |||||||
| 27310 | 5' | -53.3 | NC_005856.1 | + | 70625 | 0.66 | 0.905465 |
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Target: 5'- ---uUCUCGUgcuaUCUGUGCugguggauuuCACCAGCAc -3' miRNA: 3'- gaauAGAGCA----GGACACG----------GUGGUCGUu -5' |
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| 27310 | 5' | -53.3 | NC_005856.1 | + | 19886 | 0.7 | 0.684532 |
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Target: 5'- gUUAUCcaguUCGUCUUGcauUGCUGCCAGCAc -3' miRNA: 3'- gAAUAG----AGCAGGAC---ACGGUGGUCGUu -5' |
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| 27310 | 5' | -53.3 | NC_005856.1 | + | 55183 | 0.73 | 0.501006 |
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Target: 5'- ---uUCUCGUuaaUCUGUGCCGCCGGUu- -3' miRNA: 3'- gaauAGAGCA---GGACACGGUGGUCGuu -5' |
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| 27310 | 5' | -53.3 | NC_005856.1 | + | 38727 | 0.74 | 0.470443 |
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Target: 5'- --cAUCUCG-CCgaaUGUGCCGCCGGUAGu -3' miRNA: 3'- gaaUAGAGCaGG---ACACGGUGGUCGUU- -5' |
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| 27310 | 5' | -53.3 | NC_005856.1 | + | 92630 | 1.06 | 0.003554 |
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Target: 5'- aCUUAUCUCGUCCUGUGCCACCAGCAAc -3' miRNA: 3'- -GAAUAGAGCAGGACACGGUGGUCGUU- -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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