miRNA: 3'- -GUCCGACG----GGUGG----GCUCAUGUCaCCu -5'
miRNA: 3'- -GUCCGACGGGU----GGGCU-----CA----UGUCACCu -5'
miRNA: 3'- -GUCCGa--CGGGUGGGCuCAuGUcACCU- -5'
miRNA: 3'- -GUCCGACGGGUGGGCUCAUGUCACCU- -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 | |||||||
| 33039 | 3' | -58.7 | NC_007497.1 | + | 16846 | 0.67 | 0.378851 |
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Target: 5'- gCGGGCUGCucguCCGCCggcgCGGGUGCGG-GGc -3' miRNA: 3'- -GUCCGACG----GGUGG----GCUCAUGUCaCCu -5' |
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| 33039 | 3' | -58.7 | NC_007497.1 | + | 34576 | 0.68 | 0.361443 |
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Target: 5'- gCGGGCUGCCCGgcauCCUGAcgaccGUcggcACGGUGGc -3' miRNA: 3'- -GUCCGACGGGU----GGGCU-----CA----UGUCACCu -5' |
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| 33039 | 3' | -58.7 | NC_007497.1 | + | 33404 | 0.68 | 0.344599 |
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Target: 5'- aCGGGCgccGCCCGCCCGcGUcCGaUGGGc -3' miRNA: 3'- -GUCCGa--CGGGUGGGCuCAuGUcACCU- -5' |
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| 33039 | 3' | -58.7 | NC_007497.1 | + | 10596 | 1.08 | 0.000353 |
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Target: 5'- aCAGGCUGCCCACCCGAGUACAGUGGAu -3' miRNA: 3'- -GUCCGACGGGUGGGCUCAUGUCACCU- -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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