miRNA: 3'- ggUUCGUUUCUGGGG-----------CCUCCUcGCAC- -5'
miRNA: 3'- -GGUUCGuuUCUG----GGGCCUCC-UCgCAc -5'
miRNA: 3'- -GGUUCGUUuCUgGGGCCUCCUCGCac -5'
miRNA: 3'- -GGUUCGUUUCUGGGGCCUCCUCGCAC- -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 | |||||||
| 7473 | 3' | -55.6 | NC_001918.1 | + | 229 | 0.67 | 0.178363 |
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Target: 5'- -aGGGCGGGGGCCCUcccaggggaagGGAGGA-UGUGg -3' miRNA: 3'- ggUUCGUUUCUGGGG-----------CCUCCUcGCAC- -5' |
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| 7473 | 3' | -55.6 | NC_001918.1 | + | 671 | 0.69 | 0.125923 |
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Target: 5'- cCCAGGCucAGAUcccaCCCGGAGGuGGgGUa -3' miRNA: 3'- -GGUUCGuuUCUG----GGGCCUCC-UCgCAc -5' |
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| 7473 | 3' | -55.6 | NC_001918.1 | + | 5211 | 0.71 | 0.082474 |
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Target: 5'- aUCGGGCAG-GA-UCCGGAGGGGCGg- -3' miRNA: 3'- -GGUUCGUUuCUgGGGCCUCCUCGCac -5' |
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| 7473 | 3' | -55.6 | NC_001918.1 | + | 1112 | 1.1 | 5.1e-05 |
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Target: 5'- aCCAAGCAAAGACCCCGGAGGAGCGUGc -3' miRNA: 3'- -GGUUCGUUUCUGGGGCCUCCUCGCAC- -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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