miRNA: 3'- -UGGCGGgCUUG-CGgA-C-GCUGGaGGCG- -5'
miRNA: 3'- -UGGCGGGCUUGCGGaCGc----UGGaGGCG- -5'
miRNA: 3'- -UGGCGGGCUUGCGGACGCUGgaggcg -5'
miRNA: 3'- -UGGCGGGCUUGCGGAcGCUGGaGGCG- -5'
miRNA: 3'- -UGGCGGGCUUGCGGACGCUGGAGGCG- -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 | |||||||
| 12709 | 5' | -61.5 | NC_003349.1 | + | 82172 | 0.67 | 0.605899 |
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Target: 5'- cACCGCUgGAACuGCgUcGaCGACCgCCGCu -3' miRNA: 3'- -UGGCGGgCUUG-CGgA-C-GCUGGaGGCG- -5' |
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| 12709 | 5' | -61.5 | NC_003349.1 | + | 82241 | 0.7 | 0.41095 |
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Target: 5'- cGCCGCCUGAGCGUC-GCcuuccACCaCCGCu -3' miRNA: 3'- -UGGCGGGCUUGCGGaCGc----UGGaGGCG- -5' |
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| 12709 | 5' | -61.5 | NC_003349.1 | + | 82034 | 0.71 | 0.354931 |
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Target: 5'- cACCGCUCGAACGUCUGCGACn----- -3' miRNA: 3'- -UGGCGGGCUUGCGGACGCUGgaggcg -5' |
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| 12709 | 5' | -61.5 | NC_003349.1 | + | 82214 | 0.85 | 0.041327 |
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Target: 5'- gACCGCCCGAACGUCUaCGGCCgCCGCc -3' miRNA: 3'- -UGGCGGGCUUGCGGAcGCUGGaGGCG- -5' |
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| 12709 | 5' | -61.5 | NC_003349.1 | + | 82055 | 1.09 | 0.000808 |
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Target: 5'- cACCGCCCGAACGCCUGCGACCUCCGCc -3' miRNA: 3'- -UGGCGGGCUUGCGGACGCUGGAGGCG- -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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