miRNA: 3'- -UCUAGCGcAgCUCCUU-CAUGgUUGGc -5'
miRNA: 3'- -UC-UAGCGCAGCU------------CCUUCau-GGuUGGC- -5'
miRNA: 3'- -UCUA----GCGCAGCUCCUUCa-UGGUugGC- -5'
miRNA: 3'- -UCUAGCGCAGCUCCUUCAUGGUUGGC- -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 | |||||||
| 1152 | 3' | -52.3 | NC_001132.2 | + | 6987 | 0.66 | 0.985224 |
|
Target: 5'- uGGGUCGC-UgGAGGAAcGUGCgGGCUa -3' miRNA: 3'- -UCUAGCGcAgCUCCUU-CAUGgUUGGc -5' |
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| 1152 | 3' | -52.3 | NC_001132.2 | + | 161181 | 0.66 | 0.985224 |
|
Target: 5'- uAGaAUCGCGUCGAuguacccgucgcGGAGGaucCCcGCCGg -3' miRNA: 3'- -UC-UAGCGCAGCU------------CCUUCau-GGuUGGC- -5' |
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| 1152 | 3' | -52.3 | NC_001132.2 | + | 2064 | 0.75 | 0.664159 |
|
Target: 5'- gAGAUacggUGCGUCGAGGGAGacGCCGugCGu -3' miRNA: 3'- -UCUA----GCGCAGCUCCUUCa-UGGUugGC- -5' |
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| 1152 | 3' | -52.3 | NC_001132.2 | + | 833 | 1.09 | 0.008102 |
|
Target: 5'- uAGAUCGCGUCGAGGAAGUACCAACCGu -3' miRNA: 3'- -UCUAGCGCAGCUCCUUCAUGGUUGGC- -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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