miRNA: 3'- -GGGAGCa--AGa------------AGAUGCGaUGUGCAAG- -5'
miRNA: 3'- -GGGAGCaa-----GAAGAUG----CGAUGUGCaag -5'
miRNA: 3'- gGGAGCAAGa--AGaUGCGAUGUGcaag -5'
miRNA: 3'- -GGGAgCAAGa-AGAUGCGau----GUGCAAG- -5'
miRNA: 3'- -GGGAGCAAGAAGAUGCGAUGUGCAAG- -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 | |||||||
| 11363 | 3' | -48.6 | NC_003084.1 | + | 73864 | 0.66 | 0.998001 |
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Target: 5'- gUCCUCGaugUCgaugccacuguuaUUUGCGC-GCACGUUCa -3' miRNA: 3'- -GGGAGCa--AGa------------AGAUGCGaUGUGCAAG- -5' |
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| 11363 | 3' | -48.6 | NC_003084.1 | + | 18745 | 0.67 | 0.994822 |
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Target: 5'- gUCCUCGgcuacgaCUUCUGCuacgGCUACGCGc-- -3' miRNA: 3'- -GGGAGCaa-----GAAGAUG----CGAUGUGCaag -5' |
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| 11363 | 3' | -48.6 | NC_003084.1 | + | 756 | 0.69 | 0.979989 |
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Target: 5'- aCCUUGUUCaggUC-GCGCUGCACa--- -3' miRNA: 3'- gGGAGCAAGa--AGaUGCGAUGUGcaag -5' |
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| 11363 | 3' | -48.6 | NC_003084.1 | + | 11417 | 0.69 | 0.979989 |
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Target: 5'- aCCCUgGUUCagUUUGCGCaaucuuCGCGUUUg -3' miRNA: 3'- -GGGAgCAAGa-AGAUGCGau----GUGCAAG- -5' |
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| 11363 | 3' | -48.6 | NC_003084.1 | + | 13593 | 1.14 | 0.00552 |
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Target: 5'- aCCCUCGUUCUUCUACGCUACACGUUCg -3' miRNA: 3'- -GGGAGCAAGAAGAUGCGAUGUGCAAG- -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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