miRNA: 3'- ugGGACGUCCUUU-----UCuuCG-GCUCGgU- -5'
miRNA: 3'- -UGGGACGU-CCUUuUCUUCggCUCGgU- -5'
miRNA: 3'- ugGGaCGUCCuuUUCUUCGGCUCGgu -5'
miRNA: 3'- -UGGGACGUCCUUUUCUUCGGCUCGGU- -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 | |||||||
| 3245 | 3' | -55.1 | NC_001522.1 | + | 3412 | 0.7 | 0.081166 |
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Target: 5'- -gCCUGCAGGAAAauuguAGggGUgCGAGCgAg -3' miRNA: 3'- ugGGACGUCCUUU-----UCuuCG-GCUCGgU- -5' |
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| 3245 | 3' | -55.1 | NC_001522.1 | + | 3457 | 0.72 | 0.063993 |
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Target: 5'- uGCCCUGCAcGGGGuGGAGGaaGAGCgGa -3' miRNA: 3'- -UGGGACGU-CCUUuUCUUCggCUCGgU- -5' |
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| 3245 | 3' | -55.1 | NC_001522.1 | + | 3343 | 0.73 | 0.052114 |
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Target: 5'- -aCC-GCAGGcgGGGGAGCCGAGCa- -3' miRNA: 3'- ugGGaCGUCCuuUUCUUCGGCUCGgu -5' |
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| 3245 | 3' | -55.1 | NC_001522.1 | + | 3268 | 1.09 | 0.00005 |
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Target: 5'- gACCCUGCAGGAAAAGAAGCCGAGCCAg -3' miRNA: 3'- -UGGGACGUCCUUUUCUUCGGCUCGGU- -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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