miRNA: 3'- -GGGGGu-CCCGAAAa--------UUGGGUCUaagu -5'
miRNA: 3'- -GGGGGUCCCG-----AAAAUUGGGuCUaaGu -5'
miRNA: 3'- gGGGGUCCCGaaaau-UGGgUCUAagu -5'
miRNA: 3'- gGGGGUCCCGAaaaUUGGGucUAAGU- -5'
miRNA: 3'- -GGGGGUCCCGAAAAUUGGGUCUAAGU- -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 | |||||||
| 3232 | 3' | -51.2 | NC_001514.1 | + | 5924 | 0.68 | 0.298021 |
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Target: 5'- cCCCCCuuGGGUUUUcuaugcaacAACCCAGAa--- -3' miRNA: 3'- -GGGGGu-CCCGAAAa--------UUGGGUCUaagu -5' |
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| 3232 | 3' | -51.2 | NC_001514.1 | + | 6290 | 0.68 | 0.272497 |
|
Target: 5'- cUCCUCAGGGCgagccUUUUGGCCCuGGggCu -3' miRNA: 3'- -GGGGGUCCCG-----AAAAUUGGGuCUaaGu -5' |
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| 3232 | 3' | -51.2 | NC_001514.1 | + | 2691 | 0.69 | 0.226754 |
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Target: 5'- gCCCCAGGGCcccacuACCgGGAUg-- -3' miRNA: 3'- gGGGGUCCCGaaaau-UGGgUCUAagu -5' |
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| 3232 | 3' | -51.2 | NC_001514.1 | + | 2708 | 0.72 | 0.154666 |
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Target: 5'- gCCCUGGGGCU---GGCCCcuGUUCAa -3' miRNA: 3'- gGGGGUCCCGAaaaUUGGGucUAAGU- -5' |
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| 3232 | 3' | -51.2 | NC_001514.1 | + | 2073 | 1.12 | 0.000121 |
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Target: 5'- cCCCCCAGGGCUUUUAACCCAGAUUCAg -3' miRNA: 3'- -GGGGGUCCCGAAAAUUGGGUCUAAGU- -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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