miRNA: 3'- -ACUCC-CA-UGGaaGCAGGGGGUua---------GCC- -5'
miRNA: 3'- aCUCCCAUGGaag------------CAG-GGGGUuaGCC- -5'
miRNA: 3'- aCUCCCAUG-GAAG---------------CAG---------GGGGUUAGCC- -5'
miRNA: 3'- -ACUCCCAUGGAAGCAGGGGGUUAGCC- -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 | |||||||
| 11847 | 5' | -54.9 | NC_003266.2 | + | 8334 | 0.66 | 0.64791 |
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Target: 5'- cUGGGGaGUgACCacCGUCCCCCGuuucuucuuggCGGg -3' miRNA: 3'- -ACUCC-CA-UGGaaGCAGGGGGUua---------GCC- -5' |
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| 11847 | 5' | -54.9 | NC_003266.2 | + | 21515 | 0.68 | 0.520144 |
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Target: 5'- cGGGGGUGCCcaacggcaugcuccaGUCgCCCCAggUGGa -3' miRNA: 3'- aCUCCCAUGGaag------------CAG-GGGGUuaGCC- -5' |
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| 11847 | 5' | -54.9 | NC_003266.2 | + | 5204 | 0.7 | 0.418651 |
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Target: 5'- cGAGGGUGCgCUUCaggcucauccggcugGUCgagaaccgcUCCCGAUCGGc -3' miRNA: 3'- aCUCCCAUG-GAAG---------------CAG---------GGGGUUAGCC- -5' |
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| 11847 | 5' | -54.9 | NC_003266.2 | + | 4625 | 1.12 | 0.000486 |
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Target: 5'- uUGAGGGUACCUUCGUCCCCCAAUCGGg -3' miRNA: 3'- -ACUCCCAUGGAAGCAGGGGGUUAGCC- -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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