miRNA: 3'- -GCUAGU-ACG-------CCU----UCGUGCGU-UUCGAC- -5'
miRNA: 3'- -GCUaGUACGCcUUCGUGCGUUUcGAC- -5'
miRNA: 3'- -GCUAGUACGcc--UUCGUGCGUU-------------UCGAC- -5'
miRNA: 3'- -GCUAGUACGCCUUCGUGCGUUUCGAC- -5'
miRNA: 3'- gCUaGUAC-GCCuuCGUGCGUuuCGac -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 13000 | 3' | -51.3 | NC_003387.1 | + | 44585 | 0.66 | 0.859777 |
|
Target: 5'- gCGGUCGcUGCccggccgGGAcagcAGCGCGUAcGAGCUGg -3' miRNA: 3'- -GCUAGU-ACG-------CCU----UCGUGCGU-UUCGAC- -5' |
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| 13000 | 3' | -51.3 | NC_003387.1 | + | 45487 | 0.66 | 0.860634 |
|
Target: 5'- uCGAcCAUGCGuGAGUGCGCGAA-CUGc -3' miRNA: 3'- -GCUaGUACGCcUUCGUGCGUUUcGAC- -5' |
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| 13000 | 3' | -51.3 | NC_003387.1 | + | 48973 | 0.67 | 0.813851 |
|
Target: 5'- gCGAUCGUGCacgcGGGCAUGCGGccgucgaucgcguGGCUGu -3' miRNA: 3'- -GCUAGUACGcc--UUCGUGCGUU-------------UCGAC- -5' |
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| 13000 | 3' | -51.3 | NC_003387.1 | + | 50924 | 1.1 | 0.001781 |
|
Target: 5'- aCGAUCAUGCGGAAGCACGCAAAGCUGa -3' miRNA: 3'- -GCUAGUACGCCUUCGUGCGUUUCGAC- -5' |
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| 13000 | 3' | -51.3 | NC_003387.1 | + | 52489 | 0.66 | 0.869058 |
|
Target: 5'- uGAgCAUGuCGGggGCGCGCAu-GUc- -3' miRNA: 3'- gCUaGUAC-GCCuuCGUGCGUuuCGac -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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