miRNA: 3'- aCgGUCGGa----CUGuGUCUACGACCUac -5'
miRNA: 3'- -ACGG-----UCGGACugUGUCUAcgACCUAC- -5'
miRNA: 3'- aCGGUCGGACU----GUG---------UCU----ACGACCuaC- -5'
miRNA: 3'- -ACGGUCGGACUGUGUCUACGACCUAC- -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 | |||||||
| 9448 | 3' | -55.2 | NC_002531.1 | + | 12617 | 0.66 | 0.890664 |
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Target: 5'- aGgCGGCCgcguaGGC-UAGGUGCUGGAg- -3' miRNA: 3'- aCgGUCGGa----CUGuGUCUACGACCUac -5' |
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| 9448 | 3' | -55.2 | NC_002531.1 | + | 86526 | 0.67 | 0.80988 |
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Target: 5'- uUGCCuuuucAGCCUG--GCAGAUuaUGGAUGu -3' miRNA: 3'- -ACGG-----UCGGACugUGUCUAcgACCUAC- -5' |
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| 9448 | 3' | -55.2 | NC_002531.1 | + | 17331 | 0.69 | 0.732565 |
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Target: 5'- aGCCAGCCUGAaaucCAUgccgagccgGGAuggcUGCUGGggGg -3' miRNA: 3'- aCGGUCGGACU----GUG---------UCU----ACGACCuaC- -5' |
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| 9448 | 3' | -55.2 | NC_002531.1 | + | 104559 | 1.09 | 0.002222 |
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Target: 5'- cUGCCAGCCUGACACAGAUGCUGGAUGg -3' miRNA: 3'- -ACGGUCGGACUGUGUCUACGACCUAC- -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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