miRNA: 3'- gUGGCUGuuu--AgCUACUCGUUCAAGu -5'
miRNA: 3'- gUGGCUGuUUAGCU-ACu-CGUUCAAGu -5'
miRNA: 3'- -GUGGCuGUUUAGcUACUCGU----UCA-AGU- -5'
miRNA: 3'- -GUGGCUGuuu-AGCuaCUCGUuCAAGU- -5'
miRNA: 3'- -GUGGCUGUUUAGCUACUCGUUCAAGU- -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 | |||||||
| 16907 | 5' | -46.7 | NC_004305.1 | + | 31940 | 0.66 | 0.979332 |
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Target: 5'- aACCGAUcccguUgGGUGAGUAGGUUUg -3' miRNA: 3'- gUGGCUGuuu--AgCUACUCGUUCAAGu -5' |
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| 16907 | 5' | -46.7 | NC_004305.1 | + | 9060 | 0.67 | 0.970354 |
|
Target: 5'- aGCCGAUcAAUCGAaUGcuGCAAGUUUu -3' miRNA: 3'- gUGGCUGuUUAGCU-ACu-CGUUCAAGu -5' |
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| 16907 | 5' | -46.7 | NC_004305.1 | + | 5851 | 0.7 | 0.867829 |
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Target: 5'- cCGCCGuCAAGUCaGUGAGCAaacaGGUcUCAa -3' miRNA: 3'- -GUGGCuGUUUAGcUACUCGU----UCA-AGU- -5' |
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| 16907 | 5' | -46.7 | NC_004305.1 | + | 10777 | 0.72 | 0.80041 |
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Target: 5'- uCGCCGGCuuuuUCGgcGGGCAuGUUCAu -3' miRNA: 3'- -GUGGCUGuuu-AGCuaCUCGUuCAAGU- -5' |
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| 16907 | 5' | -46.7 | NC_004305.1 | + | 41280 | 1.11 | 0.004454 |
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Target: 5'- aCACCGACAAAUCGAUGAGCAAGUUCAa -3' miRNA: 3'- -GUGGCUGUUUAGCUACUCGUUCAAGU- -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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