miRNA: 3'- -CGUUCaGCuCCua----CaaAUGUGUGCCU- -5'
miRNA: 3'- -CGUUCa--GCUCCUaCaaau-GUGUGCCU- -5'
miRNA: 3'- -CGUUCaGCUCCUaCaaaUGUG-UGCCU- -5'
miRNA: 3'- -CGUu-CAGCUCCUACaaAuGUgUGCCu -5'
miRNA: 3'- -CGUuc--AGCUCCUacaaaUGUGUGCCU- -5'
Results 21 - 25 of 25 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 | |||||||
| 6425 | 5' | -47.6 | NC_001847.1 | + | 36013 | 0.66 | 0.999435 |
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Target: 5'- cGCGGG-CGuGGugcuggGgcUGCGCGCGGAc -3' miRNA: 3'- -CGUUCaGCuCCua----CaaAUGUGUGCCU- -5' |
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| 6425 | 5' | -47.6 | NC_001847.1 | + | 134845 | 0.66 | 0.999435 |
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Target: 5'- gGCGGGgcgCGGGGAcGgcgccCGCGCGGGc -3' miRNA: 3'- -CGUUCa--GCUCCUaCaaau-GUGUGCCU- -5' |
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| 6425 | 5' | -47.6 | NC_001847.1 | + | 49193 | 0.66 | 0.999549 |
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Target: 5'- uGCAAG-CGGGGAcGgcaACGCgACGGGg -3' miRNA: 3'- -CGUUCaGCUCCUaCaaaUGUG-UGCCU- -5' |
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| 6425 | 5' | -47.6 | NC_001847.1 | + | 97621 | 0.66 | 0.999642 |
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Target: 5'- uGCAccGUCGAGGGUGcgUcCAgGCGGc -3' miRNA: 3'- -CGUu-CAGCUCCUACaaAuGUgUGCCu -5' |
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| 6425 | 5' | -47.6 | NC_001847.1 | + | 34062 | 0.66 | 0.999718 |
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Target: 5'- cGCGuuuuUCGAGGG-----GCACGCGGAg -3' miRNA: 3'- -CGUuc--AGCUCCUacaaaUGUGUGCCU- -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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