miRNA: 3'- aAG-AGGUCA-----CAUCUUaa-----CUUGUUCCU- -5'
miRNA: 3'- -AAGAGG--UCACAUCUUAac--UUGUUCCu -5'
miRNA: 3'- aAGAGGUCAC----AUCUUAACU--------UGUuCCU- -5'
miRNA: 3'- -AAGAGGUCACAUCUUAACUUGUUCCU- -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 | |||||||
| 3495 | 5' | -45.9 | NC_001615.1 | + | 6314 | 0.66 | 0.832049 |
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Target: 5'- aUCgUCCAGUuugauGUAGGAagacaagGAACGAGGGc -3' miRNA: 3'- aAG-AGGUCA-----CAUCUUaa-----CUUGUUCCU- -5' |
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| 3495 | 5' | -45.9 | NC_001615.1 | + | 10851 | 0.66 | 0.821078 |
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Target: 5'- uUUCUCCucAGUGUAGGAUccaaAAUAAGGc -3' miRNA: 3'- -AAGAGG--UCACAUCUUAac--UUGUUCCu -5' |
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| 3495 | 5' | -45.9 | NC_001615.1 | + | 3039 | 0.71 | 0.540451 |
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Target: 5'- cUCUCCAGUGcucuUAGGAUUGGcucugugcACAuGGAu -3' miRNA: 3'- aAGAGGUCAC----AUCUUAACU--------UGUuCCU- -5' |
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| 3495 | 5' | -45.9 | NC_001615.1 | + | 6593 | 1.08 | 0.001737 |
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Target: 5'- gUUCUCCAGUGUAGAAUUGAACAAGGAc -3' miRNA: 3'- -AAGAGGUCACAUCUUAACUUGUUCCU- -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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