miRNA: 3'- caCCUUUAC---------------AAGGGAGGGUa--CCCGGC- -5'
miRNA: 3'- caCCUUUAC---------------AAGGGAGGGUa--CCCGGC- -5'
miRNA: 3'- -CACC-------UUUACAaGGGAGGGU---ACCCGGC- -5'
miRNA: 3'- -CACCUUUACAAGGGAGGGUACCCGGC- -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 | |||||||
| 2058 | 5' | -55.1 | NC_001348.1 | + | 104851 | 0.67 | 0.847593 |
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Target: 5'- -gGGAGGUGgggucgcuuuuuuuuUUCUCUCUCGaggGGGCCGc -3' miRNA: 3'- caCCUUUAC---------------AAGGGAGGGUa--CCCGGC- -5' |
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| 2058 | 5' | -55.1 | NC_001348.1 | + | 181 | 0.67 | 0.847593 |
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Target: 5'- -gGGAGGUGgggucgcuuuuuuuuUUCUCUCUCGaggGGGCCGc -3' miRNA: 3'- caCCUUUAC---------------AAGGGAGGGUa--CCCGGC- -5' |
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| 2058 | 5' | -55.1 | NC_001348.1 | + | 3003 | 0.76 | 0.368393 |
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Target: 5'- uGUGGucguguuGAAUGUaCCCUCUCAacuUGGGCCGg -3' miRNA: 3'- -CACC-------UUUACAaGGGAGGGU---ACCCGGC- -5' |
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| 2058 | 5' | -55.1 | NC_001348.1 | + | 24049 | 1.09 | 0.002813 |
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Target: 5'- cGUGGAAAUGUUCCCUCCCAUGGGCCGu -3' miRNA: 3'- -CACCUUUACAAGGGAGGGUACCCGGC- -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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