miRNA: 3'- caGCCGCAGG--------------UGCUGUaGuUUCGGUa -5'
miRNA: 3'- -CAGCCGCAGGUGcuGuaGUUU---CGGUa -5'
miRNA: 3'- cagCCGCAGG-UGCUGUAGUU-----UCG-GUA- -5'
miRNA: 3'- -CAGCCGCAG--GUG--CUGUAGuuUCGGUa -5'
miRNA: 3'- -CAGCCGCAGGUGCUGUAGUUUCGGUA- -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 | |||||||
| 27971 | 3' | -54 | NC_005886.2 | + | 5800 | 0.66 | 0.729473 |
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Target: 5'- -cCGGCGUCUgacacuggaaaucgACGACAgCcGAGCCGc -3' miRNA: 3'- caGCCGCAGG--------------UGCUGUaGuUUCGGUa -5' |
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| 27971 | 3' | -54 | NC_005886.2 | + | 37084 | 0.66 | 0.699664 |
|
Target: 5'- cGUCGGCGUCUACuuCggCAAGcgcGCCGa -3' miRNA: 3'- -CAGCCGCAGGUGcuGuaGUUU---CGGUa -5' |
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| 27971 | 3' | -54 | NC_005886.2 | + | 19959 | 0.67 | 0.654637 |
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Target: 5'- --aGGCGUUCaACGGCAUCAAcgcagGGCgCAUg -3' miRNA: 3'- cagCCGCAGG-UGCUGUAGUU-----UCG-GUA- -5' |
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| 27971 | 3' | -54 | NC_005886.2 | + | 41573 | 0.69 | 0.541978 |
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Target: 5'- cGUCGGCGUCagCGCcgGACGUUgcGGCCGg -3' miRNA: 3'- -CAGCCGCAG--GUG--CUGUAGuuUCGGUa -5' |
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| 27971 | 3' | -54 | NC_005886.2 | + | 16917 | 1.07 | 0.001438 |
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Target: 5'- cGUCGGCGUCCACGACAUCAAAGCCAUg -3' miRNA: 3'- -CAGCCGCAGGUGCUGUAGUUUCGGUA- -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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