miRNA: 3'- -GCUCGa-UGaaaGUCUUAGUCCaUACU- -5'
miRNA: 3'- gCUCGau--GAA--------AGUCUUAGUCCa-UACU- -5'
miRNA: 3'- gCUCGa---UGAAAGu----CuuAGUCCAUa--CU- -5'
miRNA: 3'- gCUCGAUGaa---AGUCu---UAGUCCAu--ACU- -5'
miRNA: 3'- -GCUCGAUGAAAGUCUUAGUCCAUACU- -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 | |||||||
| 28813 | 3' | -45.4 | NC_006146.1 | + | 117577 | 0.66 | 0.999997 |
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Target: 5'- aUGGGCcgGCgugUGGAGUCGGGgGUGAc -3' miRNA: 3'- -GCUCGa-UGaaaGUCUUAGUCCaUACU- -5' |
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| 28813 | 3' | -45.4 | NC_006146.1 | + | 66721 | 0.67 | 0.99996 |
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Target: 5'- gGAGCacguCUUccauguucUCGGAGUCAGGggGUGGg -3' miRNA: 3'- gCUCGau--GAA--------AGUCUUAGUCCa-UACU- -5' |
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| 28813 | 3' | -45.4 | NC_006146.1 | + | 23948 | 0.68 | 0.999837 |
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Target: 5'- aGGGCggcgACUUUCcccccGggUCGGGUGgggGAg -3' miRNA: 3'- gCUCGa---UGAAAGu----CuuAGUCCAUa--CU- -5' |
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| 28813 | 3' | -45.4 | NC_006146.1 | + | 153564 | 0.7 | 0.999316 |
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Target: 5'- gGAGCUGCcguggUCAGcuccGUCAGGUucuUGAc -3' miRNA: 3'- gCUCGAUGaa---AGUCu---UAGUCCAu--ACU- -5' |
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| 28813 | 3' | -45.4 | NC_006146.1 | + | 97367 | 1.11 | 0.026915 |
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Target: 5'- cCGAGCUACUUUCAGAAUCAGGUAUGAc -3' miRNA: 3'- -GCUCGAUGAAAGUCUUAGUCCAUACU- -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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