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ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# | P value |
Predicted miRNA align pattern | |||||||
30564 | 3' | -48.3 | NC_006548.1 | + | 12369 | 0.68 | 0.883845 |
Target: 5'- cGUUCAaUCcAGGCUGGGcaCUGCGCGc -3' miRNA: 3'- -CAAGUaAGcUUCGGCUCaaGAUGCGU- -5' |
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30564 | 3' | -48.3 | NC_006548.1 | + | 20899 | 0.66 | 0.938588 |
Target: 5'- ------cCGGcGGCCGAGgugCUGCGCAg -3' miRNA: 3'- caaguaaGCU-UCGGCUCaa-GAUGCGU- -5' |
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30564 | 3' | -48.3 | NC_006548.1 | + | 32690 | 1.1 | 0.002707 |
Target: 5'- cGUUCAUUCGAAGCCGAGUUCUACGCAg -3' miRNA: 3'- -CAAGUAAGCUUCGGCUCAAGAUGCGU- -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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