miRNA: 3'- uucuUCCGa-GGC-GCCGGC-CACUUGGa -5'
miRNA: 3'- -UUCUUCCGa----GGCGCCGgCCACuUGGa -5'
miRNA: 3'- uuCUUCCGaggCGCCGGCCACUUGGa -5'
miRNA: 3'- -UUCUUCCGAGGCGCCGGCCACUUGGA- -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 | |||||||
| 20424 | 3' | -59.5 | NC_004688.1 | + | 79847 | 0.67 | 0.572165 |
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Target: 5'- ---cGGGCgcCCGuCGGCCGaGUGGGCCc -3' miRNA: 3'- uucuUCCGa-GGC-GCCGGC-CACUUGGa -5' |
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| 20424 | 3' | -59.5 | NC_004688.1 | + | 44780 | 0.68 | 0.551847 |
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Target: 5'- gAGGAAGGUgcccgCCGCGGU-GGUG-GCCg -3' miRNA: 3'- -UUCUUCCGa----GGCGCCGgCCACuUGGa -5' |
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| 20424 | 3' | -59.5 | NC_004688.1 | + | 42328 | 0.7 | 0.42708 |
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Target: 5'- -cGAGGGC---GCGGUCGGUGAACUg -3' miRNA: 3'- uuCUUCCGaggCGCCGGCCACUUGGa -5' |
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| 20424 | 3' | -59.5 | NC_004688.1 | + | 14722 | 1.05 | 0.00144 |
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Target: 5'- cAAGAAGGCUCCGCGGCCGGUGAACCUa -3' miRNA: 3'- -UUCUUCCGAGGCGCCGGCCACUUGGA- -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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