miRNA: 3'- -UGAU-GAG-GCaGCACC-AGU---GAAGCCGG- -5'
miRNA: 3'- -UGau--GAGGCAGCACCAgU-GaagCCGG- -5'
miRNA: 3'- -UGAUGa-GGCAGCacCAGUGAaGcCGG- -5'
miRNA: 3'- ugaUGAGG----CAGCACC--AGUGAAG--CCGG- -5'
miRNA: 3'- -UGAUGAGGCAGCACCAGUGAAGCCGG- -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 | |||||||
| 12621 | 5' | -54.3 | NC_003345.1 | + | 6962 | 0.66 | 0.869879 |
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Target: 5'- gGCUGuCUCuCGgUGUGGcUCAaguCUUCGGCUg -3' miRNA: 3'- -UGAU-GAG-GCaGCACC-AGU---GAAGCCGG- -5' |
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| 12621 | 5' | -54.3 | NC_003345.1 | + | 29344 | 0.66 | 0.845644 |
|
Target: 5'- cACgucuCUCCGUCGUGGUgGuCgg-GGCUg -3' miRNA: 3'- -UGau--GAGGCAGCACCAgU-GaagCCGG- -5' |
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| 12621 | 5' | -54.3 | NC_003345.1 | + | 2711 | 0.67 | 0.810393 |
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Target: 5'- cACUACcgCCGUCGccGUCGCUaCcGCCg -3' miRNA: 3'- -UGAUGa-GGCAGCacCAGUGAaGcCGG- -5' |
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| 12621 | 5' | -54.3 | NC_003345.1 | + | 44293 | 0.68 | 0.772307 |
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Target: 5'- --aACUCCcgcuGUCGUGGgaUUACUUCgaGGCCc -3' miRNA: 3'- ugaUGAGG----CAGCACC--AGUGAAG--CCGG- -5' |
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| 12621 | 5' | -54.3 | NC_003345.1 | + | 34860 | 1.11 | 0.001657 |
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Target: 5'- aACUACUCCGUCGUGGUCACUUCGGCCc -3' miRNA: 3'- -UGAUGAGGCAGCACCAGUGAAGCCGG- -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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