miRNA: 3'- -GCAAgCGCGGCCacaaaGGCCCCAGc -5'
miRNA: 3'- gcaagCGCGgCC-ACaaaGGCCCCAGc -5'
miRNA: 3'- -GCAa--------GCGCGGCCacaa---AGGCCC-CAGC- -5'
miRNA: 3'- -GCAAGCGCGGCCACAAAGGCCCCAGC- -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 | |||||||
| 12326 | 3' | -57.6 | NC_003324.1 | + | 23755 | 0.66 | 0.630253 |
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Target: 5'- aCGUU-GCGCCGGaaa--UCGGGGUCc -3' miRNA: 3'- -GCAAgCGCGGCCacaaaGGCCCCAGc -5' |
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| 12326 | 3' | -57.6 | NC_003324.1 | + | 37456 | 0.66 | 0.619618 |
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Target: 5'- ----aGCGCgGGaUGgagCCGGGGUCu -3' miRNA: 3'- gcaagCGCGgCC-ACaaaGGCCCCAGc -5' |
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| 12326 | 3' | -57.6 | NC_003324.1 | + | 17685 | 0.67 | 0.577266 |
|
Target: 5'- uCGUgcucaacggCGCGCCGGggcacuaUCUGGGuGUCGa -3' miRNA: 3'- -GCAa--------GCGCGGCCacaa---AGGCCC-CAGC- -5' |
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| 12326 | 3' | -57.6 | NC_003324.1 | + | 7780 | 1.09 | 0.000765 |
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Target: 5'- uCGUUCGCGCCGGUGUUUCCGGGGUCGg -3' miRNA: 3'- -GCAAGCGCGGCCACAAAGGCCCCAGC- -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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