miRNA: 3'- aGGAGCaGCAGGCuaAGaCU-----GCCG-GG- -5'
miRNA: 3'- -AGGAGCaGC-AGGCuAAG----ACUGCCGgG- -5'
miRNA: 3'- aGGAGCa----------GCAG-GCUA---AGACUGCCGGG- -5'
miRNA: 3'- -AGGAGCAGCAGGCUaaGACUG-------CCGgg -5'
miRNA: 3'- -AGGAGCAGCAGGCUAAGACUGCCGGG- -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 | |||||||
| 4335 | 5' | -55.6 | NC_001720.1 | + | 26513 | 0.67 | 0.612802 |
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Target: 5'- aCCUCGcCGUCCGccUCgGAaccgcCGGCuCCg -3' miRNA: 3'- aGGAGCaGCAGGCuaAGaCU-----GCCG-GG- -5' |
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| 4335 | 5' | -55.6 | NC_001720.1 | + | 32323 | 0.67 | 0.601839 |
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Target: 5'- cUCCUCG-CGcUCCGcUUCcuguUGGCGGCgCu -3' miRNA: 3'- -AGGAGCaGC-AGGCuAAG----ACUGCCGgG- -5' |
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| 4335 | 5' | -55.6 | NC_001720.1 | + | 2396 | 0.67 | 0.590903 |
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Target: 5'- gCCUCGaauccaaacagUGUUaCGGUugcUCUGAUGGCCCg -3' miRNA: 3'- aGGAGCa----------GCAG-GCUA---AGACUGCCGGG- -5' |
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| 4335 | 5' | -55.6 | NC_001720.1 | + | 32426 | 0.75 | 0.224461 |
|
Target: 5'- uUCCUCGUCGUCCGAa-CUGACaacagaaGGCg- -3' miRNA: 3'- -AGGAGCAGCAGGCUaaGACUG-------CCGgg -5' |
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| 4335 | 5' | -55.6 | NC_001720.1 | + | 13347 | 1.12 | 0.000576 |
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Target: 5'- aUCCUCGUCGUCCGAUUCUGACGGCCCc -3' miRNA: 3'- -AGGAGCAGCAGGCUAAGACUGCCGGG- -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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