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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 | |||||||
| 28572 | 3' | -44.3 | NC_005946.1 | + | 45160 | 0.66 | 0.999967 |
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Target: 5'- ----aCUUCCAG-GCCAGCCu--AUGa -3' miRNA: 3'- aaaugGAAGGUCuUGGUUGGuuuUAC- -5' |
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| 28572 | 3' | -44.3 | NC_005946.1 | + | 60157 | 0.67 | 0.999803 |
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Target: 5'- -gUACCUcUCGGAGCCggUCAGGGc- -3' miRNA: 3'- aaAUGGAaGGUCUUGGuuGGUUUUac -5' |
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| 28572 | 3' | -44.3 | NC_005946.1 | + | 31272 | 0.7 | 0.997091 |
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Target: 5'- --cGCCcUCCAGAGCCuccucauCCAGGAUc -3' miRNA: 3'- aaaUGGaAGGUCUUGGuu-----GGUUUUAc -5' |
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| 28572 | 3' | -44.3 | NC_005946.1 | + | 66853 | 0.7 | 0.995841 |
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Target: 5'- --gACCUUCaGGGACCuGACCAGAGg- -3' miRNA: 3'- aaaUGGAAGgUCUUGG-UUGGUUUUac -5' |
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| 28572 | 3' | -44.3 | NC_005946.1 | + | 23878 | 0.71 | 0.995068 |
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Target: 5'- --cACCUUCCAGuAGCCu-CCGGGcgGg -3' miRNA: 3'- aaaUGGAAGGUC-UUGGuuGGUUUuaC- -5' |
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| 28572 | 3' | -44.3 | NC_005946.1 | + | 60833 | 0.72 | 0.983857 |
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Target: 5'- --gACCcucagggaUUCCAGGGCCAcagaggugGCCAAAAUGu -3' miRNA: 3'- aaaUGG--------AAGGUCUUGGU--------UGGUUUUAC- -5' |
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| 28572 | 3' | -44.3 | NC_005946.1 | + | 67741 | 0.76 | 0.903421 |
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Target: 5'- gUUUACCUccaggUCCAGGGCC-ACCAcgGUGa -3' miRNA: 3'- -AAAUGGA-----AGGUCUUGGuUGGUuuUAC- -5' |
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| 28572 | 3' | -44.3 | NC_005946.1 | + | 38244 | 0.77 | 0.880704 |
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Target: 5'- --gGCCaUCCGGAGCCcGCCAAAAa- -3' miRNA: 3'- aaaUGGaAGGUCUUGGuUGGUUUUac -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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