miRNA: 3'- aaaaaUUCUGUAGUGGUA-UGUGu---UGC- -5'
miRNA: 3'- aaaaaUUCUGUAGUGGUauGUG-UUGC- -5'
miRNA: 3'- aaaaAUUC------UGUAGUGGUa----UGUGUUGC- -5'
miRNA: 3'- aaaaauuCUGuAGUGGUAUGUGUUGC- -5'
miRNA: 3'- -AAAAAUUcUGUAGUGGUAUGUGUUGC- -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 | |||||||
| 13536 | 5' | -41.5 | NC_003436.1 | + | 27838 | 0.66 | 0.999189 |
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Target: 5'- ----aAGGAUAUUACCAUaGCACugucACGa -3' miRNA: 3'- aaaaaUUCUGUAGUGGUA-UGUGu---UGC- -5' |
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| 13536 | 5' | -41.5 | NC_003436.1 | + | 18835 | 0.67 | 0.996855 |
|
Target: 5'- ----cAAGACAUCACUAccCACuAACGu -3' miRNA: 3'- aaaaaUUCUGUAGUGGUauGUG-UUGC- -5' |
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| 13536 | 5' | -41.5 | NC_003436.1 | + | 15665 | 0.68 | 0.994397 |
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Target: 5'- ---aUAAGccaaaaACAUUACCAgcagaGCACAACGg -3' miRNA: 3'- aaaaAUUC------UGUAGUGGUa----UGUGUUGC- -5' |
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| 13536 | 5' | -41.5 | NC_003436.1 | + | 17378 | 0.69 | 0.990578 |
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Target: 5'- ------cGACuUUGCCAUGCGCAAUGu -3' miRNA: 3'- aaaaauuCUGuAGUGGUAUGUGUUGC- -5' |
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| 13536 | 5' | -41.5 | NC_003436.1 | + | 19430 | 0.93 | 0.120645 |
|
Target: 5'- gUUUUUGAaACAUCACCAUACACAACGu -3' miRNA: 3'- -AAAAAUUcUGUAGUGGUAUGUGUUGC- -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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