miRNA: 3'- -GGAAGCCGga--CugGGCGcUUGCGcGA- -5'
miRNA: 3'- ggaaGCCG-GaCUGGGCGC----------UUGCGCGA- -5'
miRNA: 3'- gGAAgCCGGACUGggCGCUUGCgCGa -5'
miRNA: 3'- -GGAAGCCGGACUGGGCGCUUGCGCGA- -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 | |||||||
| 1320 | 3' | -59 | NC_001331.1 | + | 716 | 0.67 | 0.097736 |
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Target: 5'- gCCUUCGGCaucgGugCCGCuGGCGUcCUg -3' miRNA: 3'- -GGAAGCCGga--CugGGCGcUUGCGcGA- -5' |
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| 1320 | 3' | -59 | NC_001331.1 | + | 4791 | 0.67 | 0.088755 |
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Target: 5'- ---aCGGCgCcGACCCGCGuauccuccagGGCGUGCUg -3' miRNA: 3'- ggaaGCCG-GaCUGGGCGC----------UUGCGCGA- -5' |
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| 1320 | 3' | -59 | NC_001331.1 | + | 374 | 0.79 | 0.008424 |
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Target: 5'- gCUUgGGCCUGGCuuGCGGGCGgGCc -3' miRNA: 3'- gGAAgCCGGACUGggCGCUUGCgCGa -5' |
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| 1320 | 3' | -59 | NC_001331.1 | + | 6449 | 1.08 | 2.6e-05 |
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Target: 5'- uCCUUCGGCCUGACCCGCGAACGCGCUc -3' miRNA: 3'- -GGAAGCCGGACUGGGCGCUUGCGCGA- -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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