miRNA: 3'- cuuCUaUUCGUGGGCCG------------CGca-GUGGC- -5'
miRNA: 3'- -CUUCuAUUCGUGGGCCGCGCa---------GugGC- -5'
miRNA: 3'- cUUCUAUUcguGGGCCGCGCAGUGGC- -5'
miRNA: 3'- -CUUCUAUUCGUGGGCCGCGCAGUGGC- -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 | |||||||
| 10665 | 5' | -55.3 | NC_002730.1 | + | 17621 | 0.66 | 0.609881 |
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Target: 5'- --uGAcGAGCACCCGGCcaccauuaucaaGCuugCGCCGa -3' miRNA: 3'- cuuCUaUUCGUGGGCCG------------CGca-GUGGC- -5' |
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| 10665 | 5' | -55.3 | NC_002730.1 | + | 17870 | 0.69 | 0.418017 |
|
Target: 5'- uGAAGuUGAGCAUCUGGCGCGcgguaaggggCugCGu -3' miRNA: 3'- -CUUCuAUUCGUGGGCCGCGCa---------GugGC- -5' |
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| 10665 | 5' | -55.3 | NC_002730.1 | + | 11838 | 0.7 | 0.380405 |
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Target: 5'- aGAGAUAAu--CCCGGCGUGUCGUCGa -3' miRNA: 3'- cUUCUAUUcguGGGCCGCGCAGUGGC- -5' |
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| 10665 | 5' | -55.3 | NC_002730.1 | + | 7727 | 1.08 | 0.000776 |
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Target: 5'- uGAAGAUAAGCACCCGGCGCGUCACCGc -3' miRNA: 3'- -CUUCUAUUCGUGGGCCGCGCAGUGGC- -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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