miRNA: 3'- -UCGCCgUCGCCUU-----UgACaUugCCGGU- -5'
miRNA: 3'- -UCGCCGUCGCCuu---UGaCAuUGCCGgu -5'
miRNA: 3'- uCGCCGUC--GCc--UUUGACAuUGCCGGU- -5'
Results 21 - 23 of 23 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 | |||||||
| 4187 | 5' | -55.6 | NC_001664.1 | + | 154542 | 0.67 | 0.850062 |
|
Target: 5'- gAGCGGgGGUGGGAgggaaGgUGgAugGGCCGg -3' miRNA: 3'- -UCGCCgUCGCCUU-----UgACaUugCCGGU- -5' |
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| 4187 | 5' | -55.6 | NC_001664.1 | + | 154575 | 0.69 | 0.780409 |
|
Target: 5'- cGGCGGCGGCGGuugucGCcGUcACGGUa- -3' miRNA: 3'- -UCGCCGUCGCCuu---UGaCAuUGCCGgu -5' |
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| 4187 | 5' | -55.6 | NC_001664.1 | + | 155913 | 0.67 | 0.857944 |
|
Target: 5'- cGCGGCAGgcCGuccAAACUGU-ACGGCUAu -3' miRNA: 3'- uCGCCGUC--GCc--UUUGACAuUGCCGGU- -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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