miRNA: 3'- -GUUcGGAUgUCCGU-----UCUAGUCGgCGA- -5'
miRNA: 3'- -GUUCGGa---UGUCCGu-UCuaGUCGGCGa -5'
miRNA: 3'- guUCGGAugU-CCGUUCuaGU-----------CGGCGA- -5'
miRNA: 3'- -GUUCGGAUGUCCGUUCUAGUCGGCGA- -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 | |||||||
| 740 | 3' | -54.4 | AC_000020.1 | + | 1184 | 0.67 | 0.483084 |
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Target: 5'- cCAAaCCUGgGGGCAgaaagAGGUCAGCaGCUa -3' miRNA: 3'- -GUUcGGAUgUCCGU-----UCUAGUCGgCGA- -5' |
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| 740 | 3' | -54.4 | AC_000020.1 | + | 15512 | 0.68 | 0.430164 |
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Target: 5'- aCGAGCCaaacGCGGGCccAGcgCGGUCGCg -3' miRNA: 3'- -GUUCGGa---UGUCCGu-UCuaGUCGGCGa -5' |
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| 740 | 3' | -54.4 | AC_000020.1 | + | 17334 | 0.69 | 0.390371 |
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Target: 5'- -cGGCCUugGgGGCGAGggCAuuguaggcgguGCCGCUg -3' miRNA: 3'- guUCGGAugU-CCGUUCuaGU-----------CGGCGA- -5' |
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| 740 | 3' | -54.4 | AC_000020.1 | + | 15568 | 1.08 | 0.000513 |
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Target: 5'- cCAAGCCUACAGGCAAGAUCAGCCGCUg -3' miRNA: 3'- -GUUCGGAUGUCCGUUCUAGUCGGCGA- -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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