miRNA: 3'- cucaAGAUGUCG-GGCUCGCGU-GUUGU- -5'
miRNA: 3'- -CUCAAGA--UGUCG-GGcUCGCGUGUuGU- -5'
miRNA: 3'- -CUCAAGau--------GUCGGGCUCGCGU-GUUGU- -5'
miRNA: 3'- -CUCAAGAUGUCGGGCUCGCGUGUUGU- -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 | |||||||
| 22546 | 5' | -53.4 | NC_005083.1 | + | 14466 | 0.66 | 0.987911 |
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Target: 5'- ---aUCUAUGGUaCUGAGCGCAuCAACGa -3' miRNA: 3'- cucaAGAUGUCG-GGCUCGCGU-GUUGU- -5' |
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| 22546 | 5' | -53.4 | NC_005083.1 | + | 226558 | 0.66 | 0.987911 |
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Target: 5'- uGGGUUCUguGCAGUaCCuAGCGCACG-CGa -3' miRNA: 3'- -CUCAAGA--UGUCG-GGcUCGCGUGUuGU- -5' |
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| 22546 | 5' | -53.4 | NC_005083.1 | + | 215326 | 0.71 | 0.85331 |
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Target: 5'- uGGGUUCgucguacaauCAGUCCGGGUGCAgCGGCAg -3' miRNA: 3'- -CUCAAGau--------GUCGGGCUCGCGU-GUUGU- -5' |
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| 22546 | 5' | -53.4 | NC_005083.1 | + | 113919 | 1.09 | 0.007007 |
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Target: 5'- cGAGUUCUACAGCCCGAGCGCACAACAa -3' miRNA: 3'- -CUCAAGAUGUCGGGCUCGCGUGUUGU- -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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