miRNA: 3'- -UCUaaGAGGGUCAGgUucAGCCUUuu -5'
miRNA: 3'- ucuAAGAGGGUCAGGuuCAGCCUUUU- -5'
miRNA: 3'- uCUAaGAGGGUCaGGU---------UCAGCCUUuu -5'
miRNA: 3'- uCUaAGa---GGG-UCAGGUUCAGCCUUuu -5'
miRNA: 3'- -UCUAAGAGGGUCAGGUUCAGCCUUUU- -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 | |||||||
| 10335 | 3' | -50 | NC_002687.1 | + | 321841 | 0.66 | 0.999851 |
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Target: 5'- gGGAgaCUCCCGGUCgA--UCGGGAc- -3' miRNA: 3'- -UCUaaGAGGGUCAGgUucAGCCUUuu -5' |
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| 10335 | 3' | -50 | NC_002687.1 | + | 124106 | 0.67 | 0.999531 |
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Target: 5'- --uUUUUUCUGGUCCuuGUCGGAAGAc -3' miRNA: 3'- ucuAAGAGGGUCAGGuuCAGCCUUUU- -5' |
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| 10335 | 3' | -50 | NC_002687.1 | + | 248749 | 0.67 | 0.999132 |
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Target: 5'- cGAUcCUCCCGG-CCAgcagcgaguAGUCGGGGu- -3' miRNA: 3'- uCUAaGAGGGUCaGGU---------UCAGCCUUuu -5' |
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| 10335 | 3' | -50 | NC_002687.1 | + | 304554 | 0.71 | 0.984198 |
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Target: 5'- cGAgUCcgagCCCgAGUCCGAGUCGGGGu- -3' miRNA: 3'- uCUaAGa---GGG-UCAGGUUCAGCCUUuu -5' |
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| 10335 | 3' | -50 | NC_002687.1 | + | 119653 | 1.07 | 0.027651 |
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Target: 5'- cAGAUUCUCCCAGUCCAAGUCGGAAAAg -3' miRNA: 3'- -UCUAAGAGGGUCAGGUUCAGCCUUUU- -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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