miRNA: 3'- ggaUUCGGCg--UCGGGgGAGGUGGUcc -5'
miRNA: 3'- ggAUU-CG-GCGUCGGGGGagGuGGUCC- -5'
miRNA: 3'- -GGAUU----CGGCGuc-GGG-GGaGGUGGUCC- -5'
miRNA: 3'- -GGA---UUCGGCGu------CGGGGG--------AGGuGGUCC- -5'
miRNA: 3'- -GGAUUCGGCGUCGGGGGAGGUGGUCC- -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 | |||||||
| 2292 | 3' | -59.9 | NC_001408.1 | + | 4699 | 0.66 | 0.086815 |
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Target: 5'- --gGAGCCGguuGGCCCgCUCUACCAu- -3' miRNA: 3'- ggaUUCGGCg--UCGGGgGAGGUGGUcc -5' |
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| 2292 | 3' | -59.9 | NC_001408.1 | + | 5849 | 0.67 | 0.076293 |
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Target: 5'- -gUAAuGCgCGCAGCCCCCg-C-CCGGGu -3' miRNA: 3'- ggAUU-CG-GCGUCGGGGGagGuGGUCC- -5' |
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| 2292 | 3' | -59.9 | NC_001408.1 | + | 958 | 0.68 | 0.067 |
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Target: 5'- cCCUGGcccuGCUGCucuCCCaCCcCCGCCAGGg -3' miRNA: 3'- -GGAUU----CGGCGuc-GGG-GGaGGUGGUCC- -5' |
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| 2292 | 3' | -59.9 | NC_001408.1 | + | 637 | 0.72 | 0.029416 |
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Target: 5'- uCCUcucGAGCCGCcuucaauGCCCCCaaaaccaaUCC-CCAGGu -3' miRNA: 3'- -GGA---UUCGGCGu------CGGGGG--------AGGuGGUCC- -5' |
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| 2292 | 3' | -59.9 | NC_001408.1 | + | 236 | 1.12 | 0.000009 |
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Target: 5'- cCCUAAGCCGCAGCCCCCUCCACCAGGg -3' miRNA: 3'- -GGAUUCGGCGUCGGGGGAGGUGGUCC- -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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