miRNA: 3'- -GCCUUUCCCCCUguuAgCGUCC-UCGu -5'
miRNA: 3'- gCCU--UUCCCCCUGUUagCg--UCCU--CGU- -5'
miRNA: 3'- -GCCUUU--CCCCCU-GUu-AGcGUCCUCGu -5'
miRNA: 3'- -GCCUUUCCCCC-UGUUAgCGUCcUCGU- -5'
miRNA: 3'- -GCCUUUCCCCCUGUUAGCGUCCUCGU- -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 | |||||||
| 16840 | 5' | -55.4 | NC_004194.1 | + | 3956 | 0.66 | 0.181372 |
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Target: 5'- cCGGGAGGGGGGG---UgGCGGGcGGUu -3' miRNA: 3'- -GCCUUUCCCCCUguuAgCGUCC-UCGu -5' |
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| 16840 | 5' | -55.4 | NC_004194.1 | + | 3536 | 0.66 | 0.175737 |
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Target: 5'- gGGAcaAAGGGGGACAAagGguuGGGAauGCAc -3' miRNA: 3'- gCCU--UUCCCCCUGUUagCg--UCCU--CGU- -5' |
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| 16840 | 5' | -55.4 | NC_004194.1 | + | 3334 | 0.67 | 0.154727 |
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Target: 5'- uCGGAGAcuGGGGGAgCAucUC-CAGGAGUu -3' miRNA: 3'- -GCCUUU--CCCCCU-GUu-AGcGUCCUCGu -5' |
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| 16840 | 5' | -55.4 | NC_004194.1 | + | 3642 | 0.81 | 0.010627 |
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Target: 5'- uCGGGGAGGGGGcACAGUgGCAGcAGCAg -3' miRNA: 3'- -GCCUUUCCCCC-UGUUAgCGUCcUCGU- -5' |
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| 16840 | 5' | -55.4 | NC_004194.1 | + | 4136 | 1.08 | 0.000055 |
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Target: 5'- uCGGAAAGGGGGACAAUCGCAGGAGCAu -3' miRNA: 3'- -GCCUUUCCCCCUGUUAGCGUCCUCGU- -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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