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miRNA: 3'- aagGUGGAa-----GGUGAGCGCCGa----CUGAU- -5'
miRNA: 3'- aaGGUGGaAGGUGa----GCGCCGACUGau -5'
miRNA: 3'- aaGGUGGa----AGGUGAGCGCCGACUgAU- -5'
miRNA: 3'- -AAGGUGGaAGGUGAGCGCCGACUGAU- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 30439 | 5' | -57 | NC_006548.1 | + | 29684 | 0.66 | 0.45319 |
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Target: 5'- --gCACCUgcgagcCCAUUCGCGGCcgcaaGACUGg -3' miRNA: 3'- aagGUGGAa-----GGUGAGCGCCGa----CUGAU- -5' |
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| 30439 | 5' | -57 | NC_006548.1 | + | 35042 | 0.67 | 0.42304 |
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Target: 5'- -cUCGCC-UCCGCacgugCGUGGCUGACc- -3' miRNA: 3'- aaGGUGGaAGGUGa----GCGCCGACUGau -5' |
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| 30439 | 5' | -57 | NC_006548.1 | + | 13256 | 0.68 | 0.348875 |
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Target: 5'- -cUCGCUgugucUUCACUCGCGGCUGGgUGc -3' miRNA: 3'- aaGGUGGa----AGGUGAGCGCCGACUgAU- -5' |
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| 30439 | 5' | -57 | NC_006548.1 | + | 16491 | 0.95 | 0.003277 |
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Target: 5'- cUUCCACC-UCCACUCGCGGCUGACUAc -3' miRNA: 3'- -AAGGUGGaAGGUGAGCGCCGACUGAU- -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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