miRNA: 3'- -GGCCUGcCAUGUGU--UG-GUCCCG---------GUCC- -5'
miRNA: 3'- gGCCUGCCau-----GUGUUGgUCCCGGU--CC- -5'
miRNA: 3'- -GGCCUGCCAUGUGUUGGUCCCGGUCC- -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
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| Predicted miRNA align pattern | |||||||
| 21849 | 3' | -56.8 | NC_004902.1 | + | 8629 | 0.67 | 0.540282 |
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Target: 5'- uCCGGAUcGUACGCAaaGCgCAGGGUaaucaccaaCGGGc -3' miRNA: 3'- -GGCCUGcCAUGUGU--UG-GUCCCG---------GUCC- -5' |
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| 21849 | 3' | -56.8 | NC_004902.1 | + | 27600 | 0.69 | 0.448621 |
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Target: 5'- gCGGAUGGgugguuuUACAACaAGGGCCAcaGGa -3' miRNA: 3'- gGCCUGCCau-----GUGUUGgUCCCGGU--CC- -5' |
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| 21849 | 3' | -56.8 | NC_004902.1 | + | 6575 | 1.11 | 0.000488 |
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Target: 5'- uCCGGACGGUACACAACCAGGGCCAGGc -3' miRNA: 3'- -GGCCUGCCAUGUGUUGGUCCCGGUCC- -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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