miRNA: 3'- auuucuuuugCUUAAAUUCGGG--ACCG- -5'
miRNA: 3'- auuUCUUUUGc-UUAAAUUCGGGa-----CCG- -5'
miRNA: 3'- -AUUUCUUUuGCUUaaau----UC-GGGACCG- -5'
miRNA: 3'- -AUUUCUUUUGCUUAAAUUCGGgACCG- -5'
Results 1 - 4 of 4 are showing below:
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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 | |||||||
| 28669 | 3' | -42 | NC_006066.1 | + | 1426 | 0.67 | 0.399689 |
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Target: 5'- ---------gGGAUUUAAGCCUagUGGCa -3' miRNA: 3'- auuucuuuugCUUAAAUUCGGG--ACCG- -5' |
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| 28669 | 3' | -42 | NC_006066.1 | + | 1570 | 0.7 | 0.232578 |
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Target: 5'- --cAGGAAACaaAAUUUGAGCCCaaaaagGGCu -3' miRNA: 3'- auuUCUUUUGc-UUAAAUUCGGGa-----CCG- -5' |
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| 28669 | 3' | -42 | NC_006066.1 | + | 901 | 0.72 | 0.184206 |
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Target: 5'- aUAAAGAGGuCGAAguaaaaacGGuCCCUGGCg -3' miRNA: 3'- -AUUUCUUUuGCUUaaau----UC-GGGACCG- -5' |
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| 28669 | 3' | -42 | NC_006066.1 | + | 962 | 0.96 | 0.002148 |
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Target: 5'- aUAAAGAAAACGAAUUUAAGCC-UGGCu -3' miRNA: 3'- -AUUUCUUUUGCUUAAAUUCGGgACCG- -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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