miRNA: 3'- cagUUGUUGUACagaAGU---AAUGCUGC- -5'
miRNA: 3'- cAGUUGUUGU-----------ACAGA---AGUAAUG------CUGC- -5'
miRNA: 3'- -CAGUUGUUGUACAGAAGUAAUGCUGC- -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 | |||||||
| 17746 | 5' | -43.2 | NC_004629.1 | + | 47421 | 0.66 | 1 |
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Target: 5'- --uGGCAGCAUGgg-UCAaacUUACGGCGc -3' miRNA: 3'- cagUUGUUGUACagaAGU---AAUGCUGC- -5' |
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| 17746 | 5' | -43.2 | NC_004629.1 | + | 109014 | 0.68 | 1 |
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Target: 5'- cUCAGCAACAgcacuauccauUGUCUcagUCAUUGCagcauuGACGa -3' miRNA: 3'- cAGUUGUUGU-----------ACAGA---AGUAAUG------CUGC- -5' |
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| 17746 | 5' | -43.2 | NC_004629.1 | + | 6027 | 1.12 | 0.063978 |
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Target: 5'- aGUCAACAACAUGUCUUCAUUACGACGg -3' miRNA: 3'- -CAGUUGUUGUACAGAAGUAAUGCUGC- -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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