miRNA: 3'- -AACAGCGCC-GCGguAugGGUG---------CCCGU- -5'
miRNA: 3'- aacaGCGCCGCGgUAUGGGUgCCCGu -5'
miRNA: 3'- aaCAGcGCCGCGGUaUGGGU---------------GCCCGU- -5'
miRNA: 3'- aaCAGCg-----------CCGCG-GUaUGGGUGCCCGU- -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 | |||||||
| 7579 | 3' | -60.9 | NC_001962.1 | + | 94737 | 0.66 | 0.637339 |
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Target: 5'- uUUGUCGUGGcCGCguUugUCACacucgcuauGGGCAg -3' miRNA: 3'- -AACAGCGCC-GCGguAugGGUG---------CCCGU- -5' |
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| 7579 | 3' | -60.9 | NC_001962.1 | + | 124862 | 0.67 | 0.556698 |
|
Target: 5'- ---cUGCGGCGCaAUACCCA-GGGUg -3' miRNA: 3'- aacaGCGCCGCGgUAUGGGUgCCCGu -5' |
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| 7579 | 3' | -60.9 | NC_001962.1 | + | 33652 | 0.68 | 0.521275 |
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Target: 5'- -cGUC-CGGUGCCA-GCCCAucgaguugacggccgUGGGCAg -3' miRNA: 3'- aaCAGcGCCGCGGUaUGGGU---------------GCCCGU- -5' |
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| 7579 | 3' | -60.9 | NC_001962.1 | + | 93092 | 0.73 | 0.259049 |
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Target: 5'- -cGUCGauacggccgugaGGCGCgCA-GCCCACGGGCAc -3' miRNA: 3'- aaCAGCg-----------CCGCG-GUaUGGGUGCCCGU- -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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