miRNA: 3'- uAGAGAUUUUAa---------CGACAGUUUCcaau -5'
miRNA: 3'- -UAGAGAUuUUAAC-GACAG--UUUCCAau -5'
miRNA: 3'- -UAGAGAUUUuAACGACAGUU---UCCAau -5'
miRNA: 3'- -UAGAGAUUUUAACGACAGUUUCCAAU- -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 | |||||||
| 11722 | 5' | -42.2 | NC_003157.4 | + | 36327 | 0.66 | 0.999412 |
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Target: 5'- cUCUCUAAAAUagccugagcaGCUGUCAAGGa--- -3' miRNA: 3'- uAGAGAUUUUAa---------CGACAGUUUCcaau -5' |
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| 11722 | 5' | -42.2 | NC_003157.4 | + | 7022 | 0.68 | 0.997085 |
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Target: 5'- uAUCUUUAcGAUUGaCUGUCuuAGAGGUa- -3' miRNA: 3'- -UAGAGAUuUUAAC-GACAG--UUUCCAau -5' |
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| 11722 | 5' | -42.2 | NC_003157.4 | + | 821 | 0.72 | 0.96511 |
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Target: 5'- aAUUUUUAAAuUUGCUGUCAAcuuAGGUa- -3' miRNA: 3'- -UAGAGAUUUuAACGACAGUU---UCCAau -5' |
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| 11722 | 5' | -42.2 | NC_003157.4 | + | 7058 | 1.06 | 0.021947 |
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Target: 5'- cAUCUCUAAAAUUGCUGUCAAAGGUUAc -3' miRNA: 3'- -UAGAGAUUUUAACGACAGUUUCCAAU- -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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