miRNA: 3'- -CUuuGGGC-GGAGAUGUgCCCGUcgua -5'
miRNA: 3'- cUuuGgGCGGAGa---------UGUGCCCGUCGUa -5'
miRNA: 3'- cuuUGGGCGGAGaUGUGCCCGU-CGua -5'
miRNA: 3'- -CUUUGGGCGGAGAUGUGCCCGUCGUA- -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 | |||||||
| 19723 | 3' | -56.9 | NC_004686.1 | + | 43093 | 0.71 | 0.312833 |
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Target: 5'- aGAuuCCCGuCCUCUACAgGGGCAa--- -3' miRNA: 3'- -CUuuGGGC-GGAGAUGUgCCCGUcgua -5' |
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| 19723 | 3' | -56.9 | NC_004686.1 | + | 21825 | 0.71 | 0.290195 |
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Target: 5'- cGggUgCGCCUCggcggcgcggGCGCGGGCGGCGg -3' miRNA: 3'- cUuuGgGCGGAGa---------UGUGCCCGUCGUa -5' |
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| 19723 | 3' | -56.9 | NC_004686.1 | + | 16881 | 0.72 | 0.275829 |
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Target: 5'- --cACCCGUCUUcGCGCGGGCAcGCu- -3' miRNA: 3'- cuuUGGGCGGAGaUGUGCCCGU-CGua -5' |
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| 19723 | 3' | -56.9 | NC_004686.1 | + | 52963 | 1.05 | 0.001055 |
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Target: 5'- cGAAACCCGCCUCUACACGGGCAGCAUc -3' miRNA: 3'- -CUUUGGGCGGAGAUGUGCCCGUCGUA- -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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