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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 | |||||||
| 3628 | 5' | -47.5 | NC_001650.1 | + | 73189 | 0.66 | 0.999895 |
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Target: 5'- -gGGCUGCccuccgucaccAGgaagGAGGUGAGGUCU-GAc -3' miRNA: 3'- ugUUGAUG-----------UCa---CUCCACUCUAGAaCU- -5' |
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| 3628 | 5' | -47.5 | NC_001650.1 | + | 28959 | 0.67 | 0.999539 |
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Target: 5'- --uGCcACAGgaaGAGGgggGAGAUCUUGGc -3' miRNA: 3'- uguUGaUGUCa--CUCCa--CUCUAGAACU- -5' |
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| 3628 | 5' | -47.5 | NC_001650.1 | + | 57571 | 0.68 | 0.998682 |
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Target: 5'- uGCAGCUGCGGcUGGGGcaGGGGUUggGGg -3' miRNA: 3'- -UGUUGAUGUC-ACUCCa-CUCUAGaaCU- -5' |
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| 3628 | 5' | -47.5 | NC_001650.1 | + | 39742 | 0.69 | 0.998076 |
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Target: 5'- gACAAUc-CAGUGcuGUGAGAUCUUGu -3' miRNA: 3'- -UGUUGauGUCACucCACUCUAGAACu -5' |
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| 3628 | 5' | -47.5 | NC_001650.1 | + | 91457 | 0.69 | 0.998076 |
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Target: 5'- --cGCUcucccACAGcGAGGUGAGGUCcUGAc -3' miRNA: 3'- uguUGA-----UGUCaCUCCACUCUAGaACU- -5' |
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| 3628 | 5' | -47.5 | NC_001650.1 | + | 172495 | 0.74 | 0.954497 |
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Target: 5'- -gGGCUAgAGUGAGGgGGGAUCUUa- -3' miRNA: 3'- ugUUGAUgUCACUCCaCUCUAGAAcu -5' |
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| 3628 | 5' | -47.5 | NC_001650.1 | + | 70665 | 0.75 | 0.919192 |
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Target: 5'- -aAACUGCAGgcgGAGGUGAuGGUCUUa- -3' miRNA: 3'- ugUUGAUGUCa--CUCCACU-CUAGAAcu -5' |
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| 3628 | 5' | -47.5 | NC_001650.1 | + | 39919 | 1.1 | 0.019563 |
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Target: 5'- cACAACUACAGUGAGGUGAGAUCUUGAu -3' miRNA: 3'- -UGUUGAUGUCACUCCACUCUAGAACU- -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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