miRNA: 3'- uGCUCGGGug----CGGGUCGGACGa-GACG- -5'
miRNA: 3'- ugcUCGGGUGC------------GGGU-CGGACgaGACG- -5'
miRNA: 3'- uGCUCGGGUGCGGGU-------CGGa-----CG-AGACG- -5'
miRNA: 3'- -UGCUCGGGUGCGGGUCGGACGAGACG- -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 | |||||||
| 8764 | 3' | -61.5 | NC_002371.2 | + | 3617 | 0.66 | 0.314013 |
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Target: 5'- cUGAGCUUuagccaGUUCAGCCUGCccCUGCa -3' miRNA: 3'- uGCUCGGGug----CGGGUCGGACGa-GACG- -5' |
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| 8764 | 3' | -61.5 | NC_002371.2 | + | 1341 | 0.67 | 0.270627 |
|
Target: 5'- --uAGCCCACGacuuaacagcacCCCAuGCCUGaaCUGCg -3' miRNA: 3'- ugcUCGGGUGC------------GGGU-CGGACgaGACG- -5' |
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| 8764 | 3' | -61.5 | NC_002371.2 | + | 26154 | 0.68 | 0.237654 |
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Target: 5'- gUGAGCCUGCGCCCGcaucuccGCCagaaagGCgUCUGUc -3' miRNA: 3'- uGCUCGGGUGCGGGU-------CGGa-----CG-AGACG- -5' |
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| 8764 | 3' | -61.5 | NC_002371.2 | + | 11753 | 1.11 | 0.00011 |
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Target: 5'- uACGAGCCCACGCCCAGCCUGCUCUGCa -3' miRNA: 3'- -UGCUCGGGUGCGGGUCGGACGAGACG- -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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