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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 | |||||||
| 16963 | 3' | -48.3 | NC_004322.1 | + | 2908 | 1.12 | 0.000135 |
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Target: 5'- gACAGAGAAAUCCUCAACACCAACCACg -3' miRNA: 3'- -UGUCUCUUUAGGAGUUGUGGUUGGUG- -5' |
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| 16963 | 3' | -48.3 | NC_004322.1 | + | 3414 | 0.69 | 0.253169 |
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Target: 5'- uACAGGGAugcCCUCGGCcCCAACaACa -3' miRNA: 3'- -UGUCUCUuuaGGAGUUGuGGUUGgUG- -5' |
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| 16963 | 3' | -48.3 | NC_004322.1 | + | 4512 | 0.68 | 0.325989 |
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Target: 5'- --------uUCCUCAAgacCACCAGCCACa -3' miRNA: 3'- ugucucuuuAGGAGUU---GUGGUUGGUG- -5' |
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| 16963 | 3' | -48.3 | NC_004322.1 | + | 5703 | 0.68 | 0.325989 |
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Target: 5'- gACGGcc---UCCUCAAC-CCGGCCGCc -3' miRNA: 3'- -UGUCucuuuAGGAGUUGuGGUUGGUG- -5' |
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| 16963 | 3' | -48.3 | NC_004322.1 | + | 3568 | 0.66 | 0.425129 |
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Target: 5'- uGCAGuucGAGAUCCUCAAaGCCAaguucuucaACCu- -3' miRNA: 3'- -UGUCu--CUUUAGGAGUUgUGGU---------UGGug -5' |
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| 16963 | 3' | -48.3 | NC_004322.1 | + | 426 | 0.66 | 0.43721 |
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Target: 5'- cACAGuGAcaucuUCCUCAACGCCua-CAUc -3' miRNA: 3'- -UGUCuCUuu---AGGAGUUGUGGuugGUG- -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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