miRNA: 3'- uUCCauuUCGGG----C-GGUCACGGCUCUU- -5'
miRNA: 3'- -UUCCa-UUUCGGgCGGUCACgGCUCUu -5'
miRNA: 3'- -UUCCAUUUCGGGCGGUCACGGCUCUU- -5'
miRNA: 3'- -UUCCAUUUCGGgCGgu--CACGG-CUCUU- -5'
miRNA: 3'- uuCCAUUUCGGGCGGUCA---CGGCu-CUU- -5'
Results 1 - 5 of 5 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 | |||||||
| 12351 | 3' | -56.9 | NC_003324.1 | + | 47843 | 0.67 | 0.506118 |
|
Target: 5'- cAGGc--AGCCUcacgGcCCGGUGCCGAGAAu -3' miRNA: 3'- uUCCauuUCGGG----C-GGUCACGGCUCUU- -5' |
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| 12351 | 3' | -56.9 | NC_003324.1 | + | 28970 | 0.71 | 0.303422 |
|
Target: 5'- gAAGGacGAGGCCgGCCAGUGgUGGGAc -3' miRNA: 3'- -UUCCa-UUUCGGgCGGUCACgGCUCUu -5' |
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| 12351 | 3' | -56.9 | NC_003324.1 | + | 24134 | 1.04 | 0.001159 |
|
Target: 5'- gAAGGUAAAGCCCGCCAGUGCCGAGAAg -3' miRNA: 3'- -UUCCAUUUCGGGCGGUCACGGCUCUU- -5' |
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| 12351 | 3' | -56.9 | NC_003324.1 | + | 56779 | 0.69 | 0.378288 |
|
Target: 5'- gGAGGUGGAGCCgGUaagcGUGCCgGAGGGu -3' miRNA: 3'- -UUCCAUUUCGGgCGgu--CACGG-CUCUU- -5' |
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| 12351 | 3' | -56.9 | NC_003324.1 | + | 29706 | 0.66 | 0.560091 |
|
Target: 5'- -uGGUAGAGUUCGCCGGUaccGCUGucGAAa -3' miRNA: 3'- uuCCAUUUCGGGCGGUCA---CGGCu-CUU- -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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