miRNA: 3'- cagCGaGAGUUUUAGCCG-CUCGCaGa -5'
miRNA: 3'- caGCGA-GaGUUUUAGCCGC-UCGCAGa -5'
miRNA: 3'- -CAGCGAGAGUUuua--GCCGC----UCGCAGa -5'
miRNA: 3'- -CAGCGa---------GAGUUUUAGCCGCUCGCaGa -5'
miRNA: 3'- -CAGCGAGAGUUUUAGCCGCUCGCAGA- -5'
Results 21 - 25 of 25 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 | |||||||
| 7721 | 3' | -52.3 | NC_001973.1 | + | 26535 | 0.71 | 0.868204 |
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Target: 5'- --aGCgCUCAAAGUCGGCcGAGCG-Ca -3' miRNA: 3'- cagCGaGAGUUUUAGCCG-CUCGCaGa -5' |
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| 7721 | 3' | -52.3 | NC_001973.1 | + | 28678 | 0.71 | 0.860479 |
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Target: 5'- -gCGCUgC-CAAAGUCGGCGaAGUGUCc -3' miRNA: 3'- caGCGA-GaGUUUUAGCCGC-UCGCAGa -5' |
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| 7721 | 3' | -52.3 | NC_001973.1 | + | 105349 | 0.71 | 0.852537 |
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Target: 5'- uGUUGUUCUCGAcgaagCGGCGcggaGGCGUCg -3' miRNA: 3'- -CAGCGAGAGUUuua--GCCGC----UCGCAGa -5' |
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| 7721 | 3' | -52.3 | NC_001973.1 | + | 4832 | 0.77 | 0.567132 |
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Target: 5'- uGUCGCgccacgaccgCUUAAAGUCGGCGGGCG-Cg -3' miRNA: 3'- -CAGCGa---------GAGUUUUAGCCGCUCGCaGa -5' |
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| 7721 | 3' | -52.3 | NC_001973.1 | + | 89149 | 1.08 | 0.007995 |
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Target: 5'- cGUCGCUCUCAAAAUCGGCGAGCGUCUc -3' miRNA: 3'- -CAGCGAGAGUUUUAGCCGCUCGCAGA- -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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