miRNA: 3'- gCUCGGCAGu-----CUA-UGC----------AGCGGCUGaa -5'
miRNA: 3'- gCUCGGCAGUC---UAu--------------GCAGCGGCUGaa -5'
miRNA: 3'- -GCUCGGCAGuCUaUGCaGCGGCUGaa -5'
Results 1 - 3 of 3 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 | |||||||
| 12266 | 5' | -55.2 | NC_003309.1 | + | 20208 | 0.67 | 0.641016 |
|
Target: 5'- gGAGCCGUCcucgucGAUcACGgcgaaccgcuUCGCCGACa- -3' miRNA: 3'- gCUCGGCAGu-----CUA-UGC----------AGCGGCUGaa -5' |
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| 12266 | 5' | -55.2 | NC_003309.1 | + | 22750 | 0.72 | 0.366773 |
|
Target: 5'- aGGGCCGUCAGuuuGUcgaucucgcgcugauCGUCGCCGGCg- -3' miRNA: 3'- gCUCGGCAGUC---UAu--------------GCAGCGGCUGaa -5' |
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| 12266 | 5' | -55.2 | NC_003309.1 | + | 48226 | 0.73 | 0.324344 |
|
Target: 5'- uCGAGCCGUCcGA-GCGcCGCUGACg- -3' miRNA: 3'- -GCUCGGCAGuCUaUGCaGCGGCUGaa -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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