miRNA: 3'- -UUGaa-CCCgAGC-UGGCCCA---------------UCGGCUC- -5'
miRNA: 3'- -UUGAa-CCC-------GAGCUGGCC-CAUCGGCUc -5'
miRNA: 3'- uuGAAC-CCGAGCUGGCCca--UCGGCUc -5'
miRNA: 3'- -UUGaACC-CGAGCUGGCCCAUCGGCUC- -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 | |||||||
| 1364 | 3' | -58.6 | NC_001335.1 | + | 18875 | 0.66 | 0.486852 |
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Target: 5'- gAACgacGGG-UCGaACCGGGUgucggucuuggucuuGGCCGAGa -3' miRNA: 3'- -UUGaa-CCCgAGC-UGGCCCA---------------UCGGCUC- -5' |
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| 1364 | 3' | -58.6 | NC_001335.1 | + | 14499 | 0.66 | 0.471758 |
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Target: 5'- gAACUcaGGGagcgugcCUCGGCUGGuGUGGCCGAc -3' miRNA: 3'- -UUGAa-CCC-------GAGCUGGCC-CAUCGGCUc -5' |
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| 1364 | 3' | -58.6 | NC_001335.1 | + | 31061 | 0.69 | 0.336682 |
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Target: 5'- -uCUUGcGGUUCGGCCGGcucgGGCCGGu -3' miRNA: 3'- uuGAAC-CCGAGCUGGCCca--UCGGCUc -5' |
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| 1364 | 3' | -58.6 | NC_001335.1 | + | 20999 | 0.92 | 0.007286 |
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Target: 5'- cAAC-UGGuGCUCGACCGGGUAGCCGAGg -3' miRNA: 3'- -UUGaACC-CGAGCUGGCCCAUCGGCUC- -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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