miRNA: 3'- -UAGAa-CG---ACUAGCCCCACaa------UGGCUa -5'
miRNA: 3'- uagaACGACu---AGCC-CCACAAUGGCUa -5'
miRNA: 3'- uaGAACG-ACUAGCCCCACaAUGGCua -5'
miRNA: 3'- -UAGAACGACUAGCCCCACAAUGGCUA- -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 | |||||||
| 23250 | 3' | -52.9 | NC_005259.1 | + | 45447 | 0.68 | 0.734146 |
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Target: 5'- gAUCUcgGUccuUGAUCGGGGUGccgaacggGCCGAg -3' miRNA: 3'- -UAGAa-CG---ACUAGCCCCACaa------UGGCUa -5' |
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| 23250 | 3' | -52.9 | NC_005259.1 | + | 47576 | 0.73 | 0.450878 |
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Target: 5'- ---cUGCUGucccUCGGcGGUGUUGCCGAa -3' miRNA: 3'- uagaACGACu---AGCC-CCACAAUGGCUa -5' |
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| 23250 | 3' | -52.9 | NC_005259.1 | + | 31519 | 0.79 | 0.219257 |
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Target: 5'- -aCUUGCuUGAUCGGGGUGgUGCCGu- -3' miRNA: 3'- uaGAACG-ACUAGCCCCACaAUGGCua -5' |
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| 23250 | 3' | -52.9 | NC_005259.1 | + | 37895 | 1.05 | 0.003671 |
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Target: 5'- gAUCUUGCUGAUCGGGGUGUUACCGAUg -3' miRNA: 3'- -UAGAACGACUAGCCCCACAAUGGCUA- -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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