miRNA: 3'- -GAAGCucCUGUCcuUACC----ACUUCGCC- -5'
miRNA: 3'- gaaGCUCCUG-------UCCUUACCACU---UCGcc -5'
miRNA: 3'- -GAAGCUCCU-GUCCUU--------ACCAcUUCGCC- -5'
miRNA: 3'- gaAGCUCCUg-----UCCUUA-CCACUUCGCC- -5'
miRNA: 3'- -GAAGCUCCUGuCCUUACCACUUCGCC- -5'
Results 1 - 5 of 5 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 17625 | 3' | -51.3 | NC_004466.2 | + | 38418 | 0.66 | 0.877141 |
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Target: 5'- aCUUCGuuGGCAGu-GUGGgaaaUGAAGUGGa -3' miRNA: 3'- -GAAGCucCUGUCcuUACC----ACUUCGCC- -5' |
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| 17625 | 3' | -51.3 | NC_004466.2 | + | 38385 | 0.7 | 0.675505 |
|
Target: 5'- --cCGAGGAUcuccccaAGGAGUGGUGGgauGGCa- -3' miRNA: 3'- gaaGCUCCUG-------UCCUUACCACU---UCGcc -5' |
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| 17625 | 3' | -51.3 | NC_004466.2 | + | 17574 | 0.76 | 0.368773 |
|
Target: 5'- uCUUCGAGGAuCAGGAAcuccaggcUGGU-AAGUGGa -3' miRNA: 3'- -GAAGCUCCU-GUCCUU--------ACCAcUUCGCC- -5' |
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| 17625 | 3' | -51.3 | NC_004466.2 | + | 586 | 0.79 | 0.244508 |
|
Target: 5'- -aUCGGGGGuugacaAGGGAUcGGUGAAGCGGu -3' miRNA: 3'- gaAGCUCCUg-----UCCUUA-CCACUUCGCC- -5' |
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| 17625 | 3' | -51.3 | NC_004466.2 | + | 38528 | 1.02 | 0.007023 |
|
Target: 5'- aCUUCGAGGAC-GGAAUGGUGAAGCGGg -3' miRNA: 3'- -GAAGCUCCUGuCCUUACCACUUCGCC- -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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