miRNA: 3'- guCGCGUUGGAGuUGCU------AGGCAguuu -5'
miRNA: 3'- gUCGCGUUGGag---UUGCUAGG-CAGUuu -5'
miRNA: 3'- gUCGCGUUGga----GUUGCUA----GGCAGUUU- -5'
miRNA: 3'- -GUCGCGUUGGAGUUGCUAGGCAGUUU- -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 | |||||||
| 33687 | 5' | -51.6 | NC_011452.1 | + | 6286 | 0.66 | 0.299937 |
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Target: 5'- -uGCGCGACCUC-ACGGgacacuUCCGUg--- -3' miRNA: 3'- guCGCGUUGGAGuUGCU------AGGCAguuu -5' |
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| 33687 | 5' | -51.6 | NC_011452.1 | + | 6190 | 0.7 | 0.175982 |
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Target: 5'- gGGCGCGACCguccaGAUGAUCUuGUCAu- -3' miRNA: 3'- gUCGCGUUGGag---UUGCUAGG-CAGUuu -5' |
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| 33687 | 5' | -51.6 | NC_011452.1 | + | 6107 | 0.72 | 0.118168 |
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Target: 5'- uGGCGCAGCagagcgCAACGGUcuuaCCGUCGAGg -3' miRNA: 3'- gUCGCGUUGga----GUUGCUA----GGCAGUUU- -5' |
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| 33687 | 5' | -51.6 | NC_011452.1 | + | 4537 | 1.06 | 0.00021 |
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Target: 5'- cCAGCGCAACCUCAACGAUCCGUCAAAg -3' miRNA: 3'- -GUCGCGUUGGAGUUGCUAGGCAGUUU- -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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