miRNA: 3'- -CG-AGuuCG-GCCCGUCA----CCGAGAUCua -5'
miRNA: 3'- -CGAGU---UCGGCc-CGUCaCCGAGaUCUa -5'
miRNA: 3'- -CGAGUu---CGGC-CCGuCACCGAG--------AUCUA- -5'
miRNA: 3'- cgaGUUCGGCCCGu--CACCg---AGAUCUA- -5'
miRNA: 3'- -CGAGUUCGGCCCGUCACCGAGAUCUA- -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 | |||||||
| 16653 | 5' | -56.8 | NC_004156.1 | + | 65188 | 0.66 | 0.927022 |
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Target: 5'- cGCaUCu-GCuCGGGCGGUaucuGGCUCUGGc- -3' miRNA: 3'- -CG-AGuuCG-GCCCGUCA----CCGAGAUCua -5' |
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| 16653 | 5' | -56.8 | NC_004156.1 | + | 210236 | 0.67 | 0.891425 |
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Target: 5'- cGCUCAcgcAGCCGcaGCAGgGGCUCcAGGa -3' miRNA: 3'- -CGAGU---UCGGCc-CGUCaCCGAGaUCUa -5' |
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| 16653 | 5' | -56.8 | NC_004156.1 | + | 224104 | 0.67 | 0.870606 |
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Target: 5'- gGCUCGguuuGCUGuGGCuGUGGCUCauuuacauUAGAUg -3' miRNA: 3'- -CGAGUu---CGGC-CCGuCACCGAG--------AUCUA- -5' |
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| 16653 | 5' | -56.8 | NC_004156.1 | + | 77324 | 0.69 | 0.770366 |
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Target: 5'- --cCGAGCCGGGCuacGUGGgcaaUCUGGGUc -3' miRNA: 3'- cgaGUUCGGCCCGu--CACCg---AGAUCUA- -5' |
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| 16653 | 5' | -56.8 | NC_004156.1 | + | 170134 | 1.07 | 0.004255 |
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Target: 5'- uGCUCAAGCCGGGCAGUGGCUCUAGAUu -3' miRNA: 3'- -CGAGUUCGGCCCGUCACCGAGAUCUA- -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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