miRNA: 3'- -GGUGuuaGUGAAGUACUUUU--------CUGUUu -5'
miRNA: 3'- -GGUGUUAGUGAaGUACU---------UuuCUGUUu -5'
miRNA: 3'- gGUGUUAgUGAAgUACUUUUCuGUUU- -5'
miRNA: 3'- -GGUGUUAGUGAAGUACUUUUCUGUUU- -5'
Results 1 - 4 of 4 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 | |||||||
| 21802 | 3' | -41.1 | NC_004827.1 | + | 39132 | 0.66 | 0.999964 |
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Target: 5'- cCCACcg-CACUUUAUGAGGGucugaaacGACAAu -3' miRNA: 3'- -GGUGuuaGUGAAGUACUUUU--------CUGUUu -5' |
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| 21802 | 3' | -41.1 | NC_004827.1 | + | 27203 | 0.69 | 0.999307 |
|
Target: 5'- gCCACAAUCGCUaCGUGGuugccgaucAucGGCGAc -3' miRNA: 3'- -GGUGUUAGUGAaGUACU---------UuuCUGUUu -5' |
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| 21802 | 3' | -41.1 | NC_004827.1 | + | 953 | 0.72 | 0.99059 |
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Target: 5'- gUACAAUgGCUUgAUGAAAAGcCAAAg -3' miRNA: 3'- gGUGUUAgUGAAgUACUUUUCuGUUU- -5' |
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| 21802 | 3' | -41.1 | NC_004827.1 | + | 33375 | 1.11 | 0.019565 |
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Target: 5'- uCCACAAUCACUUCAUGAAAAGACAAAa -3' miRNA: 3'- -GGUGUUAGUGAAGUACUUUUCUGUUU- -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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