miRNA: 3'- -UAAUUuUGUUACCGGG-GGgacc--ACGG- -5'
miRNA: 3'- uaauuuugUUACCGGGGGG-----------ACCACGG- -5'
miRNA: 3'- uaAUUUUGUUaCCGGGGgGACCACgG- -5'
miRNA: 3'- -UAAUUUUGUUACCGGGGGGACCACGG- -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 | |||||||
| 55 | 5' | -52 | AC_000003.1 | + | 28967 | 0.68 | 0.576323 |
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Target: 5'- gGUUAAcGCGAUGGCCCaCCaucgucUGCCa -3' miRNA: 3'- -UAAUUuUGUUACCGGG-GGgacc--ACGG- -5' |
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| 55 | 5' | -52 | AC_000003.1 | + | 14179 | 0.7 | 0.462484 |
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Target: 5'- -------aAAUGGUCCCCCggcagcgcgccUGGUGCUg -3' miRNA: 3'- uaauuuugUUACCGGGGGG-----------ACCACGG- -5' |
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| 55 | 5' | -52 | AC_000003.1 | + | 16331 | 0.78 | 0.151346 |
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Target: 5'- -cUGAAGCAAaGGCCCCgCUGGUGgUa -3' miRNA: 3'- uaAUUUUGUUaCCGGGGgGACCACgG- -5' |
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| 55 | 5' | -52 | AC_000003.1 | + | 16431 | 1.1 | 0.000751 |
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Target: 5'- cAUUAAAACAAUGGCCCCCCUGGUGCCc -3' miRNA: 3'- -UAAUUUUGUUACCGGGGGGACCACGG- -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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