miRNA: 3'- cGCACGGUaa--CGGAGa-----GAGCgCuUGG- -5'
miRNA: 3'- cgcaCGGuaaC-GGAGAGAGCG-----------CUUGG- -5'
miRNA: 3'- cgCACGGUAa-----------CGGAGAGAGc-------GCUUGG- -5'
miRNA: 3'- -CGCACGGUAACGGAGAGAGCGCUUGG- -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 | |||||||
| 9429 | 3' | -53.7 | NC_002531.1 | + | 122526 | 0.66 | 0.959247 |
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Target: 5'- cCGUGCCAgaggGCCUUcacgccCUCGgGuACCu -3' miRNA: 3'- cGCACGGUaa--CGGAGa-----GAGCgCuUGG- -5' |
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| 9429 | 3' | -53.7 | NC_002531.1 | + | 35002 | 0.67 | 0.927446 |
|
Target: 5'- ---cGCCuggGuCCUCUCUCGCuuccagucccuGAGCCg -3' miRNA: 3'- cgcaCGGuaaC-GGAGAGAGCG-----------CUUGG- -5' |
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| 9429 | 3' | -53.7 | NC_002531.1 | + | 18177 | 0.67 | 0.908881 |
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Target: 5'- -gGUGCCGUgagcagcaccgaGCCUCUCUCauguggaaCGAGCUa -3' miRNA: 3'- cgCACGGUAa-----------CGGAGAGAGc-------GCUUGG- -5' |
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| 9429 | 3' | -53.7 | NC_002531.1 | + | 36192 | 1.14 | 0.002107 |
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Target: 5'- cGCGUGCCAUUGCCUCUCUCGCGAACCc -3' miRNA: 3'- -CGCACGGUAACGGAGAGAGCGCUUGG- -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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