miRNA: 3'- -CUGUGU----AGU-GCC-CAGACGCGCAcGUA- -5'
miRNA: 3'- cUGUGUAGUgC---------CCA------GACGCGCACGUa -5'
miRNA: 3'- cuGUGUaGUGCC-CAGA---CGCGCACGUA- -5'
miRNA: 3'- -CUGUGUaGUGCCCa--GACGCGCACgUa -5'
miRNA: 3'- -CUGUGUAGUGCCCAGACGCGCACGUA- -5'
Results 1 - 5 of 5 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 | |||||||
| 11295 | 5' | -56.3 | NC_003083.1 | + | 24306 | 0.66 | 0.839083 |
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Target: 5'- cGACGCAgcucUCGuCGGcGUUUGCGCGUuCAUu -3' miRNA: 3'- -CUGUGU----AGU-GCC-CAGACGCGCAcGUA- -5' |
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| 11295 | 5' | -56.3 | NC_003083.1 | + | 78354 | 0.66 | 0.821871 |
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Target: 5'- uGCACGUCAgGuuaauuuguGGUaaagaaCUGCGCGUGCGc -3' miRNA: 3'- cUGUGUAGUgC---------CCA------GACGCGCACGUa -5' |
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| 11295 | 5' | -56.3 | NC_003083.1 | + | 21060 | 0.67 | 0.775807 |
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Target: 5'- -gUACAaCGCGGcGUCUucaGCGUGUGCGUc -3' miRNA: 3'- cuGUGUaGUGCC-CAGA---CGCGCACGUA- -5' |
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| 11295 | 5' | -56.3 | NC_003083.1 | + | 8517 | 0.69 | 0.632737 |
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Target: 5'- aGACACAcCAUGGGcacUUGCGCGUGgAg -3' miRNA: 3'- -CUGUGUaGUGCCCa--GACGCGCACgUa -5' |
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| 11295 | 5' | -56.3 | NC_003083.1 | + | 109634 | 1.06 | 0.002602 |
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Target: 5'- cGACACAUCACGGGUCUGCGCGUGCAUa -3' miRNA: 3'- -CUGUGUAGUGCCCAGACGCGCACGUA- -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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