miRNA: 3'- -GGGUGG---------CGCGUUACag-CGC-CGUGUGC- -5'
miRNA: 3'- -GGGUGgCGCGuUACaGCgCCGUGUgc -5'
miRNA: 3'- -GGGUGGCGCGUUACAGCGCCGUGUGC- -5'
miRNA: 3'- gGGUGGCGCguUaCAGCG---------------CCGUGUGc -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 |
| Predicted miRNA align pattern | |||||||
| 2185 | 3' | -57.4 | NC_001396.1 | + | 771 | 0.66 | 0.131516 |
|
Target: 5'- gCCUACUuuugcaauuGUGCAGUGggaGUGcGCACGCGg -3' miRNA: 3'- -GGGUGG---------CGCGUUACag-CGC-CGUGUGC- -5' |
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| 2185 | 3' | -57.4 | NC_001396.1 | + | 2645 | 0.67 | 0.123411 |
|
Target: 5'- gCCCACgGCGUcGUGcCG-GGCACGg- -3' miRNA: 3'- -GGGUGgCGCGuUACaGCgCCGUGUgc -5' |
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| 2185 | 3' | -57.4 | NC_001396.1 | + | 3433 | 1.1 | 0.000028 |
|
Target: 5'- cCCCACCGCGCAAUGUCGCGGCACACGu -3' miRNA: 3'- -GGGUGGCGCGUUACAGCGCCGUGUGC- -5' |
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| 2185 | 3' | -57.4 | NC_001396.1 | + | 5310 | 0.71 | 0.057233 |
|
Target: 5'- gCCGCCGCGguG-GUCGCgcugcugguccuggcGGUACACa -3' miRNA: 3'- gGGUGGCGCguUaCAGCG---------------CCGUGUGc -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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