miRNA: 3'- -CUAAUGGu------GUAGUUGCcaAGGU------------CGGG- -5'
miRNA: 3'- cuaaUGGUGUa-GUUGCCAA-GGUCGgg -5'
miRNA: 3'- cuaaUGGUGUAGUUGCCaaGG---------UCGGG- -5'
miRNA: 3'- cuaaUGGUG---UAGUUGCCAAGgUCGGG- -5'
Results 21 - 24 of 24 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 | |||||||
| 12640 | 3' | -49.7 | NC_003345.1 | + | 21233 | 0.66 | 0.972382 |
|
Target: 5'- cGAUUACCuccacguCGUCAGCG--UCCAcgaugagggacuGCCCg -3' miRNA: 3'- -CUAAUGGu------GUAGUUGCcaAGGU------------CGGG- -5' |
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| 12640 | 3' | -49.7 | NC_003345.1 | + | 34076 | 0.66 | 0.980398 |
|
Target: 5'- ---cACCACGgaCGAUGGUUuCCAGCg- -3' miRNA: 3'- cuaaUGGUGUa-GUUGCCAA-GGUCGgg -5' |
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| 12640 | 3' | -49.7 | NC_003345.1 | + | 27746 | 0.66 | 0.980398 |
|
Target: 5'- ---aGCCACGUCAGCGGg-CCgaauguuggGGUCUg -3' miRNA: 3'- cuaaUGGUGUAGUUGCCaaGG---------UCGGG- -5' |
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| 12640 | 3' | -49.7 | NC_003345.1 | + | 75405 | 0.77 | 0.500816 |
|
Target: 5'- ---gGCCGCgagGUCGGCGGUUC-AGCCCu -3' miRNA: 3'- cuaaUGGUG---UAGUUGCCAAGgUCGGG- -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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