miRNA: 3'- aaGAuaUGCCCCUGUA---CGAGCGgaga -5'
miRNA: 3'- aAGauAUGCCCCUGUa--------CG------------AGCGGAGA- -5'
miRNA: 3'- aagauaUGCCCCuGUACgAGCGGAGA- -5'
miRNA: 3'- -AAGAUAUGCCCCUGUACGAGCGGAGA- -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 | |||||||
| 31789 | 3' | -54.5 | NC_006938.1 | + | 63561 | 0.66 | 0.765936 |
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Target: 5'- -aCUcgAUGGGGACGUucaGCUCGCg--- -3' miRNA: 3'- aaGAuaUGCCCCUGUA---CGAGCGgaga -5' |
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| 31789 | 3' | -54.5 | NC_006938.1 | + | 50511 | 0.66 | 0.745091 |
|
Target: 5'- gUCacUACGGGGACGgagaaccugGCagaggucacugaUCGCCUCUu -3' miRNA: 3'- aAGauAUGCCCCUGUa--------CG------------AGCGGAGA- -5' |
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| 31789 | 3' | -54.5 | NC_006938.1 | + | 46657 | 0.68 | 0.635723 |
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Target: 5'- -----cGCGGGGcCGUG-UCGCCUCUc -3' miRNA: 3'- aagauaUGCCCCuGUACgAGCGGAGA- -5' |
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| 31789 | 3' | -54.5 | NC_006938.1 | + | 4662 | 1.06 | 0.001916 |
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Target: 5'- gUUCUAUACGGGGACAUGCUCGCCUCUg -3' miRNA: 3'- -AAGAUAUGCCCCUGUACGAGCGGAGA- -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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