miRNA: 3'- -CCGUCCUgaGCGUCuGC---UCGCCGGCG- -5'
miRNA: 3'- -CCGuCCUGAGCGUC--------------UGC---UCgCCG-GCG- -5'
miRNA: 3'- ccgUCCUGag--CGUCuGCUCgCCGGCG- -5'
miRNA: 3'- cCG-UCCUgAGCGUCUG---CUCGCCgGCG- -5'
miRNA: 3'- cCGUCCUgagCGUCugCU-CGcCGGCG- -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 132 | 3' | -59.9 | AC_000006.1 | + | 17644 | 0.71 | 0.15798 |
|
Target: 5'- gGGCGGGGa-CGCGG-CGcacGGCGGUCGCc -3' miRNA: 3'- -CCGUCCUgaGCGUCuGC---UCGCCGGCG- -5' |
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| 132 | 3' | -59.9 | AC_000006.1 | + | 23156 | 0.68 | 0.286881 |
|
Target: 5'- gGGUuGGGCUCGCAGgugccguugggcugGCGuugGGgGGCaCGCg -3' miRNA: 3'- -CCGuCCUGAGCGUC--------------UGC---UCgCCG-GCG- -5' |
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| 132 | 3' | -59.9 | AC_000006.1 | + | 24313 | 0.68 | 0.274876 |
|
Target: 5'- --gAGGACgugaGCGG-CGAGgGGCUGCu -3' miRNA: 3'- ccgUCCUGag--CGUCuGCUCgCCGGCG- -5' |
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| 132 | 3' | -59.9 | AC_000006.1 | + | 24434 | 0.66 | 0.368408 |
|
Target: 5'- aGCuGGGGgUUGCAGACcagGAGCGG-UGCg -3' miRNA: 3'- cCG-UCCUgAGCGUCUG---CUCGCCgGCG- -5' |
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| 132 | 3' | -59.9 | AC_000006.1 | + | 30605 | 0.66 | 0.359833 |
|
Target: 5'- cGCAGGA---GCAGugGAuGCaGCCGUu -3' miRNA: 3'- cCGUCCUgagCGUCugCU-CGcCGGCG- -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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