miRNA: 3'- -CCUUUUACAACGCGGUCAGCUCUUUU- -5'
miRNA: 3'- -CCUUuUACAACG----CGGUCA--------GCUCUUUU- -5'
miRNA: 3'- -CCUUUUacaa-CGCGGUCaGCUCUUUU- -5'
miRNA: 3'- -CCUUUUacaa-CGCGGUCaGCUCUUUU- -5'
miRNA: 3'- -CCUUUUacaa-CGCGGUCaGCUCUUUU- -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 | |||||||
| 3344 | 5' | -46.1 | NC_001550.1 | + | 1110 | 1.1 | 0.000566 |
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Target: 5'- aGGAAAAUGUUGCGCCAGUCGAGAAAAg -3' miRNA: 3'- -CCUUUUACAACGCGGUCAGCUCUUUU- -5' |
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| 3344 | 5' | -46.1 | NC_001550.1 | + | 1115 | 0.74 | 0.261426 |
|
Target: 5'- aGGGAuAUGUUGCccugGCCAGUgaggcgugCGAGAAAGg -3' miRNA: 3'- -CCUUuUACAACG----CGGUCA--------GCUCUUUU- -5' |
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| 3344 | 5' | -46.1 | NC_001550.1 | + | 7713 | 0.68 | 0.522709 |
|
Target: 5'- cGGGAAAcauucGCGCCGG-CGGGAAAGu -3' miRNA: 3'- -CCUUUUacaa-CGCGGUCaGCUCUUUU- -5' |
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| 3344 | 5' | -46.1 | NC_001550.1 | + | 8070 | 0.68 | 0.522709 |
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Target: 5'- cGGGAAAcauucGCGCCGG-CGGGAAAGu -3' miRNA: 3'- -CCUUUUacaa-CGCGGUCaGCUCUUUU- -5' |
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| 3344 | 5' | -46.1 | NC_001550.1 | + | 8460 | 0.68 | 0.522709 |
|
Target: 5'- cGGGAAAcauucGCGCCGG-CGGGAAAGu -3' miRNA: 3'- -CCUUUUacaa-CGCGGUCaGCUCUUUU- -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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