miRNA: 3'- cuauacAGCGCGCGGCUAuAACUGga -5'
miRNA: 3'- cuaUACAGCGCGCgGCUAUaa---------CUGGa -5'
miRNA: 3'- cuauaCagCGCGCGG-CUAUA--ACUGGa -5'
miRNA: 3'- cuauaCaGCGCGCGG-CUAuaACUGGa -5'
miRNA: 3'- -CUAUACAGCGCGCGGCUAUAACUGGA- -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 | |||||||
| 1296 | 5' | -50.7 | NC_001317.1 | + | 17321 | 0.66 | 0.791461 |
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Target: 5'- -----aUCGUGCGCCGGU-UUGACa- -3' miRNA: 3'- cuauacAGCGCGCGGCUAuAACUGga -5' |
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| 1296 | 5' | -50.7 | NC_001317.1 | + | 6283 | 0.67 | 0.756677 |
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Target: 5'- --gGUGUCGUGCGgCGAUGgucagaggugaGGCCg -3' miRNA: 3'- cuaUACAGCGCGCgGCUAUaa---------CUGGa -5' |
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| 1296 | 5' | -50.7 | NC_001317.1 | + | 19636 | 0.67 | 0.747724 |
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Target: 5'- ----cGggGCGCGCCuGAUAUccUGACCa -3' miRNA: 3'- cuauaCagCGCGCGG-CUAUA--ACUGGa -5' |
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| 1296 | 5' | -50.7 | NC_001317.1 | + | 8236 | 0.67 | 0.713428 |
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Target: 5'- ----aGcCGUGCGCCaGAUggUGACCa -3' miRNA: 3'- cuauaCaGCGCGCGG-CUAuaACUGGa -5' |
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| 1296 | 5' | -50.7 | NC_001317.1 | + | 27118 | 1.09 | 0.001439 |
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Target: 5'- gGAUAUGUCGCGCGCCGAUAUUGACCUg -3' miRNA: 3'- -CUAUACAGCGCGCGGCUAUAACUGGA- -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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