miRNA: 3'- cGCAUgUCGCag----GAgCAGGCGACCaa -5'
miRNA: 3'- -CGCAUGU-CGCAGG-----AGCAGgCGACCaa -5'
miRNA: 3'- cGCAuGUCGCA---GGaGCa-GGCGACCAa -5'
miRNA: 3'- -CGCAUGUCGCAGGAGCAGGCGACCAA- -5'
Results 1 - 4 of 4 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 | |||||||
| 11380 | 5' | -56.8 | NC_003084.1 | + | 83831 | 0.66 | 0.824391 |
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Target: 5'- aUGUAgAGCGcuuuaaCUgGUCCGCUGGa- -3' miRNA: 3'- cGCAUgUCGCag----GAgCAGGCGACCaa -5' |
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| 11380 | 5' | -56.8 | NC_003084.1 | + | 100002 | 0.66 | 0.80671 |
|
Target: 5'- aGUGUACGuGCGUCUaaaaaUUGUUgGCUGGa- -3' miRNA: 3'- -CGCAUGU-CGCAGG-----AGCAGgCGACCaa -5' |
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| 11380 | 5' | -56.8 | NC_003084.1 | + | 25877 | 0.66 | 0.778979 |
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Target: 5'- aCGUcCAGCGUgcaCC-CGggCCGCUGGUg -3' miRNA: 3'- cGCAuGUCGCA---GGaGCa-GGCGACCAa -5' |
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| 11380 | 5' | -56.8 | NC_003084.1 | + | 63051 | 1.08 | 0.001868 |
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Target: 5'- cGCGUACAGCGUCCUCGUCCGCUGGUUa -3' miRNA: 3'- -CGCAUGUCGCAGGAGCAGGCGACCAA- -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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