miRNA: 3'- uGgCCGGGCU---CGGcCGGCU-UGGCGUu -5'
miRNA: 3'- -UGGCCggGCUcGGCCggCUUGGCGUU- -5'
miRNA: 3'- -UGGCCGGGcUCGGCCGGcUUGGcGUu -5'
miRNA: 3'- -UGGCCGgGC-UCGGCCGGCuUGGCGUU- -5'
Results 21 - 24 of 24 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 | |||||||
| 1380 | 5' | -64.8 | NC_001335.1 | + | 5895 | 0.67 | 0.218851 |
|
Target: 5'- uCgGGCCUGGucuGCCuGCCGAuACCGCAc -3' miRNA: 3'- uGgCCGGGCU---CGGcCGGCU-UGGCGUu -5' |
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| 1380 | 5' | -64.8 | NC_001335.1 | + | 4839 | 0.66 | 0.241785 |
|
Target: 5'- aGCCGGaaCGAuUCGGuuGAGCCGUAAc -3' miRNA: 3'- -UGGCCggGCUcGGCCggCUUGGCGUU- -5' |
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| 1380 | 5' | -64.8 | NC_001335.1 | + | 2406 | 0.67 | 0.218851 |
|
Target: 5'- cGCCGGCCU-AGCCGGCCcAGCU-CAc -3' miRNA: 3'- -UGGCCGGGcUCGGCCGGcUUGGcGUu -5' |
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| 1380 | 5' | -64.8 | NC_001335.1 | + | 596 | 0.72 | 0.091996 |
|
Target: 5'- gGCCGGCaCGaAGUCGGUCG-GCCGCAGa -3' miRNA: 3'- -UGGCCGgGC-UCGGCCGGCuUGGCGUU- -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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