miRNA: 3'- ucuUC-GGUGGaaaa-UCuuCCA--UCGGG- -5'
miRNA: 3'- ucUUCGg------UGGaAAAUCuuCCa-UCGGG- -5'
miRNA: 3'- uCuuCGGUGGAAaAUcUUCCAUCGGG- -5'
miRNA: 3'- -UCUUCGGUGGAAAAUCUUCCAUCGGG- -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 | |||||||
| 15186 | 5' | -49.1 | NC_003790.1 | + | 3747 | 0.66 | 0.4063 |
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Target: 5'- --cAGuCCACCaaagaAGggGGUccAGCCCa -3' miRNA: 3'- ucuUC-GGUGGaaaa-UCuuCCA--UCGGG- -5' |
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| 15186 | 5' | -49.1 | NC_003790.1 | + | 78 | 0.66 | 0.394973 |
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Target: 5'- -uGAGCagugaaaGCC-UUUGGggGGcgAGCCCc -3' miRNA: 3'- ucUUCGg------UGGaAAAUCuuCCa-UCGGG- -5' |
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| 15186 | 5' | -49.1 | NC_003790.1 | + | 5538 | 0.73 | 0.12891 |
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Target: 5'- uGggGCUACCUUcUAaAAGGUGGCUUc -3' miRNA: 3'- uCuuCGGUGGAAaAUcUUCCAUCGGG- -5' |
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| 15186 | 5' | -49.1 | NC_003790.1 | + | 5572 | 1.12 | 0.000119 |
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Target: 5'- cAGAAGCCACCUUUUAGAAGGUAGCCCc -3' miRNA: 3'- -UCUUCGGUGGAAAAUCUUCCAUCGGG- -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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