miRNA: 3'- gAUUgGCGCAGCAUa--UAGUUUaucuc -5'
miRNA: 3'- gaUUGGCG-------CAGCAUa--------UAGU--UUAUCUC- -5'
miRNA: 3'- gaUUGGCGCAGCAuaUaGUU------UAUCUc -5'
miRNA: 3'- gAUUGGCGCaGcAUAUAGu---UUAUCUC- -5'
miRNA: 3'- -GAUUGGCGCAGCAUAUAGUUUAUCUC- -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 | |||||||
| 30953 | 3' | -43.3 | NC_006556.1 | + | 4019 | 0.66 | 0.991757 |
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Target: 5'- gUGAgCGCGUCGUGgucGUCAAAc---- -3' miRNA: 3'- gAUUgGCGCAGCAUa--UAGUUUaucuc -5' |
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| 30953 | 3' | -43.3 | NC_006556.1 | + | 16868 | 0.67 | 0.981975 |
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Target: 5'- -gGACCGCcacauauGUCGUAgaggccaaaGUCAccGAUAGAGg -3' miRNA: 3'- gaUUGGCG-------CAGCAUa--------UAGU--UUAUCUC- -5' |
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| 30953 | 3' | -43.3 | NC_006556.1 | + | 969 | 0.69 | 0.952557 |
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Target: 5'- -cAGCCGCGUCGUcgGcCAGcacgugGUGGAa -3' miRNA: 3'- gaUUGGCGCAGCAuaUaGUU------UAUCUc -5' |
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| 30953 | 3' | -43.3 | NC_006556.1 | + | 7281 | 0.7 | 0.915609 |
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Target: 5'- gUGGCCGCG-C-UAUAUCcgguGAUAGAGg -3' miRNA: 3'- gAUUGGCGCaGcAUAUAGu---UUAUCUC- -5' |
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| 30953 | 3' | -43.3 | NC_006556.1 | + | 6765 | 1.12 | 0.00401 |
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Target: 5'- cCUAACCGCGUCGUAUAUCAAAUAGAGg -3' miRNA: 3'- -GAUUGGCGCAGCAUAUAGUUUAUCUC- -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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