miRNA: 3'- -GACACCGG-------------CUCACC-GUCuuC--CGGGgu -5'
miRNA: 3'- gaCACCGg-CUCACCGucuUCCGGGgu -5'
miRNA: 3'- gacaCCGGCUca--CCG------UCUUCCGGGGu -5'
miRNA: 3'- -GACACCGGCUCACCGUCUUCCGGGGU- -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 | |||||||
| 14990 | 3' | -60.6 | NC_003690.1 | + | 7558 | 0.67 | 0.084663 |
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Target: 5'- cCUGUGGCCuguggcaugagugGAGUGGuCAGggGaaGCCUg- -3' miRNA: 3'- -GACACCGG-------------CUCACC-GUCuuC--CGGGgu -5' |
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| 14990 | 3' | -60.6 | NC_003690.1 | + | 9385 | 0.67 | 0.082293 |
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Target: 5'- -gGUGGUgaGAGUGGCu--AGGCCCa- -3' miRNA: 3'- gaCACCGg-CUCACCGucuUCCGGGgu -5' |
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| 14990 | 3' | -60.6 | NC_003690.1 | + | 10721 | 0.67 | 0.082293 |
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Target: 5'- ---aGGCCGAacugGGCguuauaAGGAGGCCCCc -3' miRNA: 3'- gacaCCGGCUca--CCG------UCUUCCGGGGu -5' |
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| 14990 | 3' | -60.6 | NC_003690.1 | + | 7636 | 1.07 | 0.000031 |
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Target: 5'- uCUGUGGCCGAGUGGCAGAAGGCCCCAc -3' miRNA: 3'- -GACACCGGCUCACCGUCUUCCGGGGU- -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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