miRNA: 3'- ucGGCggUGGUCUUGGUGGUGGUCUc -5'
miRNA: 3'- ucGGCGGUGG---UCUUGGUGGUGG---UCUC- -5'
miRNA: 3'- -UCGGCGGUGG---UCUUGGUGGUGG---UCUC- -5'
miRNA: 3'- -UCGGCGGUGGUCUUGGUGGUGGUCUC- -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 | |||||||
| 12035 | 3' | -58.5 | NC_003287.2 | + | 2404 | 0.79 | 0.006403 |
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Target: 5'- -aCCGgaACCAGAGCCACCACCGGAa -3' miRNA: 3'- ucGGCggUGGUCUUGGUGGUGGUCUc -5' |
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| 12035 | 3' | -58.5 | NC_003287.2 | + | 1879 | 0.8 | 0.0052 |
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Target: 5'- -aCCGCCACCcucAGAACCGCCACCcucAGAGc -3' miRNA: 3'- ucGGCGGUGG---UCUUGGUGGUGG---UCUC- -5' |
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| 12035 | 3' | -58.5 | NC_003287.2 | + | 2367 | 0.89 | 0.000915 |
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Target: 5'- gAGCCGCCACCcucAGAACCGCCACCcucAGAGc -3' miRNA: 3'- -UCGGCGGUGG---UCUUGGUGGUGG---UCUC- -5' |
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| 12035 | 3' | -58.5 | NC_003287.2 | + | 2322 | 1.08 | 2e-05 |
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Target: 5'- gAGCCGCCACCAGAACCACCACCAGAGc -3' miRNA: 3'- -UCGGCGGUGGUCUUGGUGGUGGUCUC- -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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