miRNA: 3'- uaaCCAUCGUAGCUGUGU---------------UGAuUGCC- -5'
miRNA: 3'- uaACCauCGUAGCUGuGUUGAUUGcc -5'
miRNA: 3'- uaaCCA------------UCGUAGCUGUgUUGAUUGCC- -5'
miRNA: 3'- -UAACCAUCGUAGCUGUGUUGAUUGCC- -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
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| Predicted miRNA align pattern | |||||||
| 10237 | 5' | -46.9 | NC_002668.1 | + | 30454 | 0.66 | 0.972977 |
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Target: 5'- --aGGUAGCAUCGGUAUAucauuauugauaauuGCU-ACGGu -3' miRNA: 3'- uaaCCAUCGUAGCUGUGU---------------UGAuUGCC- -5' |
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| 10237 | 5' | -46.9 | NC_002668.1 | + | 31610 | 0.66 | 0.964488 |
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Target: 5'- -gUGGcuGCAUCGAC-CAACUGAUu- -3' miRNA: 3'- uaACCauCGUAGCUGuGUUGAUUGcc -5' |
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| 10237 | 5' | -46.9 | NC_002668.1 | + | 27573 | 0.66 | 0.960452 |
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Target: 5'- --aGGUgucauaaacaauGGUAUCGGCGgAAUUAAUGGu -3' miRNA: 3'- uaaCCA------------UCGUAGCUGUgUUGAUUGCC- -5' |
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| 10237 | 5' | -46.9 | NC_002668.1 | + | 31581 | 1.09 | 0.004736 |
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Target: 5'- uAUUGGUAGCAUCGACACAACUAACGGc -3' miRNA: 3'- -UAACCAUCGUAGCUGUGUUGAUUGCC- -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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