miRNA: 3'- -UGgUCGUCGUCUu------UG-GugCGAGGAUa -5'
miRNA: 3'- -UGGuCGUCGUCUUUGGUGCGAGGaua -5'
miRNA: 3'- uGGUCGUCGUCUUUGGUg---CGAGGaua -5'
miRNA: 3'- uGGUCGUCGUCUUU------GGUGCGAG-GAUA- -5'
miRNA: 3'- -UGGUCGUCGUCUUUGGUGCGAGGAUA- -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 | |||||||
| 21000 | 5' | -54.5 | NC_004735.1 | + | 45623 | 0.66 | 0.872673 |
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Target: 5'- cACgAGCGGCAGAcaaacuuGCuCugGCUCUUGc -3' miRNA: 3'- -UGgUCGUCGUCUu------UG-GugCGAGGAUa -5' |
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| 21000 | 5' | -54.5 | NC_004735.1 | + | 286 | 0.68 | 0.813915 |
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Target: 5'- uGCC-GCGGUGGAAACCGUGCUUCa-- -3' miRNA: 3'- -UGGuCGUCGUCUUUGGUGCGAGGaua -5' |
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| 21000 | 5' | -54.5 | NC_004735.1 | + | 80530 | 0.69 | 0.766387 |
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Target: 5'- uCCGGUGGCGGAAGCCGgugaGCUUCa-- -3' miRNA: 3'- uGGUCGUCGUCUUUGGUg---CGAGGaua -5' |
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| 21000 | 5' | -54.5 | NC_004735.1 | + | 122548 | 0.71 | 0.641526 |
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Target: 5'- uCCGGCGGUAGAGAuguuucUCAUGCUCuCUAUa -3' miRNA: 3'- uGGUCGUCGUCUUU------GGUGCGAG-GAUA- -5' |
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| 21000 | 5' | -54.5 | NC_004735.1 | + | 163 | 1.05 | 0.004728 |
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Target: 5'- cACCAGCAGCAGAAACCACGCUCCUAUc -3' miRNA: 3'- -UGGUCGUCGUCUUUGGUGCGAGGAUA- -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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