miRNA: 3'- -GUCCGACUUgAAGUGG---CGAGa--GACGC- -5'
miRNA: 3'- gUCCGACUUGAag-------UG-GCGAGAGa--CGc -5'
miRNA: 3'- -GUCCgacuuGAAGUGGCGaGAGACGc -5'
miRNA: 3'- guCCGACUUGaaGUGGCGAg----AGACGC- -5'
miRNA: 3'- -GUCCGACUUGAAGUGGCGAGAGACGC- -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 | |||||||
| 1008 | 3' | -54.5 | NC_000924.1 | + | 1321 | 0.66 | 0.786591 |
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Target: 5'- aUAGGCUGAA-UUCGCCauuGUUCcucCUGCGu -3' miRNA: 3'- -GUCCGACUUgAAGUGG---CGAGa--GACGC- -5' |
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| 1008 | 3' | -54.5 | NC_000924.1 | + | 19077 | 0.66 | 0.735193 |
|
Target: 5'- aAGGCUGAACUggagaaacaGCuUGCUCUCgcaGCa -3' miRNA: 3'- gUCCGACUUGAag-------UG-GCGAGAGa--CGc -5' |
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| 1008 | 3' | -54.5 | NC_000924.1 | + | 25568 | 0.66 | 0.735193 |
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Target: 5'- gCAGGacgucCUUCACUGC-CUCUGCa -3' miRNA: 3'- -GUCCgacuuGAAGUGGCGaGAGACGc -5' |
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| 1008 | 3' | -54.5 | NC_000924.1 | + | 14674 | 0.68 | 0.614897 |
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Target: 5'- -uGGCUGAACa-CACCGUUgaugaUCUGCGc -3' miRNA: 3'- guCCGACUUGaaGUGGCGAg----AGACGC- -5' |
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| 1008 | 3' | -54.5 | NC_000924.1 | + | 25734 | 1.09 | 0.001196 |
|
Target: 5'- uCAGGCUGAACUUCACCGCUCUCUGCGg -3' miRNA: 3'- -GUCCGACUUGAAGUGGCGAGAGACGC- -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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