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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 | |||||||
| 12342 | 3' | -46.9 | NC_003324.1 | + | 19537 | 1.08 | 0.008253 |
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Target: 5'- gGUUGAAAUACACGCGUCUCGGCUUUGc -3' miRNA: 3'- -CAACUUUAUGUGCGCAGAGCCGAAAC- -5' |
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| 12342 | 3' | -46.9 | NC_003324.1 | + | 48746 | 0.68 | 0.970086 |
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Target: 5'- --cGAGAUGCGCagccaGCGUCUCcuGGCUc-- -3' miRNA: 3'- caaCUUUAUGUG-----CGCAGAG--CCGAaac -5' |
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| 12342 | 3' | -46.9 | NC_003324.1 | + | 34432 | 0.68 | 0.976249 |
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Target: 5'- cGUUGAGGcuUACgaGCGCGagCUCGGCa--- -3' miRNA: 3'- -CAACUUU--AUG--UGCGCa-GAGCCGaaac -5' |
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| 12342 | 3' | -46.9 | NC_003324.1 | + | 16511 | 0.67 | 0.985514 |
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Target: 5'- cGUUGAuGUGCAgcggaucggccugUGCGUgCUCGGCg--- -3' miRNA: 3'- -CAACUuUAUGU-------------GCGCA-GAGCCGaaac -5' |
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| 12342 | 3' | -46.9 | NC_003324.1 | + | 32180 | 0.67 | 0.985708 |
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Target: 5'- -gUGAuugccgACGCGCGUCgugcgCGGCa--- -3' miRNA: 3'- caACUuua---UGUGCGCAGa----GCCGaaac -5' |
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| 12342 | 3' | -46.9 | NC_003324.1 | + | 27598 | 0.66 | 0.987543 |
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Target: 5'- --cGAGGguuuuUGCuGCGCGUC-CGGCUUUa -3' miRNA: 3'- caaCUUU-----AUG-UGCGCAGaGCCGAAAc -5' |
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| 12342 | 3' | -46.9 | NC_003324.1 | + | 30628 | 0.66 | 0.987543 |
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Target: 5'- -cUGGAGUAgagcaGCGCGUCgcagCGGCa--- -3' miRNA: 3'- caACUUUAUg----UGCGCAGa---GCCGaaac -5' |
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| 12342 | 3' | -46.9 | NC_003324.1 | + | 23397 | 0.66 | 0.990663 |
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Target: 5'- ------uUugACGCG-CUCGGCUUUc -3' miRNA: 3'- caacuuuAugUGCGCaGAGCCGAAAc -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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