miRNA: 3'- -CGGCACG---------UGGACGG-CGGUUUCca-GUa -5'
miRNA: 3'- cGGCaCGUGGa---CGGCGGuUUCCAGUa -5'
miRNA: 3'- -CG-GCACgUGGACG-GCGG---UUUCCAGua -5'
miRNA: 3'- -CGGCACGUGGACGGCGGUUUCCAGUA- -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 | |||||||
| 746 | 3' | -57.5 | AC_000020.1 | + | 2261 | 0.66 | 0.386985 |
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Target: 5'- uGCCGUGCuuaggccuaACCUGCCuGCUGGAGaagCAa -3' miRNA: 3'- -CGGCACG---------UGGACGG-CGGUUUCca-GUa -5' |
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| 746 | 3' | -57.5 | AC_000020.1 | + | 16706 | 0.67 | 0.350818 |
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Target: 5'- cCCG-GCGCCcagcGCCGUC-AGGGUCAc -3' miRNA: 3'- cGGCaCGUGGa---CGGCGGuUUCCAGUa -5' |
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| 746 | 3' | -57.5 | AC_000020.1 | + | 4801 | 0.71 | 0.195665 |
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Target: 5'- uGCaCGUGgGCCUGCaCGCUgguGAGGGUCc- -3' miRNA: 3'- -CG-GCACgUGGACG-GCGG---UUUCCAGua -5' |
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| 746 | 3' | -57.5 | AC_000020.1 | + | 22317 | 1.08 | 0.000261 |
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Target: 5'- cGCCGUGCACCUGCCGCCAAAGGUCAUa -3' miRNA: 3'- -CGGCACGUGGACGGCGGUUUCCAGUA- -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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