miRNA: 3'- -UUCUGCGAAGGUGGGAGAGGCCGUCA- -5'
miRNA: 3'- -UUCUGCGaaGGUGGGAGA----GGCCGUCa -5'
miRNA: 3'- uUCUGCGA---AGGUGGGA-----GAGGCCGUCA- -5'
miRNA: 3'- uUCUgCGaAGGuGGGAGAGGCCGUCA- -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 | |||||||
| 4346 | 3' | -58.5 | NC_001720.1 | + | 20461 | 1.05 | 0.00056 |
|
Target: 5'- aAAGACGCUUCCACCCUCUCCGGCAGUa -3' miRNA: 3'- -UUCUGCGAAGGUGGGAGAGGCCGUCA- -5' |
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| 4346 | 3' | -58.5 | NC_001720.1 | + | 32566 | 0.76 | 0.091113 |
|
Target: 5'- gGAGGCGCcaUCACCCUCUgcagCCGGCGGg -3' miRNA: 3'- -UUCUGCGaaGGUGGGAGA----GGCCGUCa -5' |
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| 4346 | 3' | -58.5 | NC_001720.1 | + | 17537 | 0.73 | 0.143542 |
|
Target: 5'- cAGGCGCUgucUCCGCUCUauuucCUCCGGUGGUa -3' miRNA: 3'- uUCUGCGA---AGGUGGGA-----GAGGCCGUCA- -5' |
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| 4346 | 3' | -58.5 | NC_001720.1 | + | 6659 | 0.66 | 0.443353 |
|
Target: 5'- cGGA-GC-UCCuCUCUCUUCGGCAGUc -3' miRNA: 3'- uUCUgCGaAGGuGGGAGAGGCCGUCA- -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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