miRNA: 3'- gCCUUUUGGAGCuuCCGg-----------ACGAAGag -5'
miRNA: 3'- gCCu--UuuGGAGCUUCCGGACgaAGAg -5'
miRNA: 3'- -GCCU-----UUUGGaGCUUCCGGaCGaaGAG- -5'
miRNA: 3'- -GCCU--UUUGGAgCUUCCGGa-CGa-AGAG- -5'
miRNA: 3'- -GCCUUUUGGAGCUUCCGGACGAAGAG- -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 | |||||||
| 8789 | 3' | -52 | NC_002484.1 | + | 50152 | 0.67 | 0.81704 |
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Target: 5'- uGGGAAGCCUUGccGGCacagugggagaaUGCUUCa- -3' miRNA: 3'- gCCUUUUGGAGCuuCCGg-----------ACGAAGag -5' |
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| 8789 | 3' | -52 | NC_002484.1 | + | 11285 | 0.67 | 0.80933 |
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Target: 5'- aGGcccAggUCUCGAGGGCCUGa-UCUa -3' miRNA: 3'- gCCu--UuuGGAGCUUCCGGACgaAGAg -5' |
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| 8789 | 3' | -52 | NC_002484.1 | + | 5662 | 0.69 | 0.704325 |
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Target: 5'- uCGGGgcgauAGACCgCGAAGGCCaGCcgCUCc -3' miRNA: 3'- -GCCU-----UUUGGaGCUUCCGGaCGaaGAG- -5' |
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| 8789 | 3' | -52 | NC_002484.1 | + | 14390 | 0.7 | 0.670806 |
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Target: 5'- uCGGAugGGGCCUgGAGGGCCgaGUaaUCUCg -3' miRNA: 3'- -GCCU--UUUGGAgCUUCCGGa-CGa-AGAG- -5' |
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| 8789 | 3' | -52 | NC_002484.1 | + | 932 | 1.12 | 0.001361 |
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Target: 5'- aCGGAAAACCUCGAAGGCCUGCUUCUCg -3' miRNA: 3'- -GCCUUUUGGAGCUUCCGGACGAAGAG- -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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