miRNA: 3'- -AAG-GCGUCGA--------------AGAAGUA-UugGCGGUA- -5'
miRNA: 3'- aaGGCGUCGaagaAGUAuUGGCGGua -5'
miRNA: 3'- aAggCGUCGAAGAa-----GUaUugGCGGUa -5'
miRNA: 3'- -AAGGCGUCGAAGAAGUAUUGGCGGUA- -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 | |||||||
| 16929 | 5' | -52.5 | NC_004313.1 | + | 9654 | 0.66 | 0.710321 |
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Target: 5'- gUUCgCGCAGCUccagcacaugaagcUUUUCGUuAugCGCCAUa -3' miRNA: 3'- -AAG-GCGUCGA--------------AGAAGUA-UugGCGGUA- -5' |
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| 16929 | 5' | -52.5 | NC_004313.1 | + | 8141 | 0.66 | 0.690592 |
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Target: 5'- -gCCGCAGCg---UCAUcACCGCUg- -3' miRNA: 3'- aaGGCGUCGaagaAGUAuUGGCGGua -5' |
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| 16929 | 5' | -52.5 | NC_004313.1 | + | 11630 | 0.68 | 0.584556 |
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Target: 5'- gUuuGCAGCUUCUguacagCGaAugCGCCAg -3' miRNA: 3'- aAggCGUCGAAGAa-----GUaUugGCGGUa -5' |
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| 16929 | 5' | -52.5 | NC_004313.1 | + | 29217 | 1.04 | 0.001892 |
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Target: 5'- aUUCCGCAGCUUCUUCAUAACCGCCAUg -3' miRNA: 3'- -AAGGCGUCGAAGAAGUAUUGGCGGUA- -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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