miRNA: 3'- cUUCCCGA------------AUU--UGACGUAAGUAAAuu -5'
miRNA: 3'- -CUU-CC-CGAAUUUGACGUAAGUaaauu -5'
miRNA: 3'- -CUUCCCGAaUUUGACguaaGUAAAUU- -5'
miRNA: 3'- cuuCCCGAAUUUGA---------CGUAAGUAaauu -5'
miRNA: 3'- -CUUCCCGAAUUUGACGUAAGUAAAUU- -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 | |||||||
| 23552 | 5' | -42.3 | NC_005260.1 | + | 53717 | 0.67 | 1 |
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Target: 5'- aGAGGGCUuucgcccucucuUGAuuACUGCAUUUGUUUc- -3' miRNA: 3'- cUUCCCGA------------AUU--UGACGUAAGUAAAuu -5' |
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| 23552 | 5' | -42.3 | NC_005260.1 | + | 142667 | 0.66 | 1 |
|
Target: 5'- aGAAuGGuGUUUGGACUGCGUUUAa---- -3' miRNA: 3'- -CUU-CC-CGAAUUUGACGUAAGUaaauu -5' |
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| 23552 | 5' | -42.3 | NC_005260.1 | + | 213212 | 0.72 | 0.999921 |
|
Target: 5'- aGAAGGGCUaAGACUGacucCAUUUAGg -3' miRNA: 3'- -CUUCCCGAaUUUGACguaaGUAAAUU- -5' |
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| 23552 | 5' | -42.3 | NC_005260.1 | + | 100557 | 0.73 | 0.999696 |
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Target: 5'- --cGGGCUUGAGCUuguaccauuGCAUUCAUa--- -3' miRNA: 3'- cuuCCCGAAUUUGA---------CGUAAGUAaauu -5' |
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| 23552 | 5' | -42.3 | NC_005260.1 | + | 212984 | 1.08 | 0.088868 |
|
Target: 5'- cGAAGGGCUUAAACUGCAUUCAUUUAAc -3' miRNA: 3'- -CUUCCCGAAUUUGACGUAAGUAAAUU- -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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