miRNA: 3'- -CGUU--CGaCGCACCg--GUGC-------AGCCACUU- -5'
miRNA: 3'- -CGUUCGACGCACCGGUGCAGCCACUU- -5'
miRNA: 3'- -CgUUCGACGCACCGGUgCA---GCC-ACUu -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 |
| Predicted miRNA align pattern | |||||||
| 2342 | 5' | -56.9 | NC_001416.1 | + | 7822 | 0.67 | 0.490836 |
|
Target: 5'- gGCAGcuGCgGCGUGGagaCACGcugaccaUCGGUGAGg -3' miRNA: 3'- -CGUU--CGaCGCACCg--GUGC-------AGCCACUU- -5' |
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| 2342 | 5' | -56.9 | NC_001416.1 | + | 10830 | 1.07 | 0.000665 |
|
Target: 5'- uGCAAGCUGCGUGGCCACGUCGGUGAAc -3' miRNA: 3'- -CGUUCGACGCACCGGUGCAGCCACUU- -5' |
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| 2342 | 5' | -56.9 | NC_001416.1 | + | 14952 | 0.67 | 0.502329 |
|
Target: 5'- cGgGAGCUGUGUGGCCA-GUgccCGGaUGGc -3' miRNA: 3'- -CgUUCGACGCACCGGUgCA---GCC-ACUu -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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