miRNA: 3'- -UCGGUGG-UACG----UGGCCGGGGa---AGGUc -5'
miRNA: 3'- -UCGGUgGUACGUGGCCGGGGAAGGUC- -5'
miRNA: 3'- uCGGUGGUa---CgUGGCCGGGGAa----GGuc -5'
Results 1 - 3 of 3 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 7443 | 5' | -60.7 | NC_001902.1 | + | 16161 | 0.7 | 0.122929 |
|
Target: 5'- cAGCCACUuGUGCcaagGCCGGCCCCacugUUCAc -3' miRNA: 3'- -UCGGUGG-UACG----UGGCCGGGGa---AGGUc -5' |
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| 7443 | 5' | -60.7 | NC_001902.1 | + | 18957 | 0.96 | 0.001041 |
|
Target: 5'- cAGCCA-CAUGCACCGGCCCCUUCCAGu -3' miRNA: 3'- -UCGGUgGUACGUGGCCGGGGAAGGUC- -5' |
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| 7443 | 5' | -60.7 | NC_001902.1 | + | 23363 | 0.69 | 0.145974 |
|
Target: 5'- cGCCACCAagacGgGCCGGCCCUUgggggCCc- -3' miRNA: 3'- uCGGUGGUa---CgUGGCCGGGGAa----GGuc -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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