miRNA: 3'- gCUGUA--UGU-CCCGCGgUu----CGCUGUCU- -5'
miRNA: 3'- gCUGU-------AUguCCCGCGGUuCG-CUGUCU- -5'
miRNA: 3'- gcUGUa--UGUCC-----CGCGGUUCGCUGUCu -5'
miRNA: 3'- gCUGUAUGU-----CCCGCGGUU-CG-CUGUCU- -5'
miRNA: 3'- -GCUGUAUGUCCCGCGGUUCGCUGUCU- -5'
Results 1 - 5 of 5 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 | |||||||
| 576 | 3' | -54.7 | AC_000015.1 | + | 24090 | 0.66 | 0.610829 |
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Target: 5'- gGGCAUcgGCGcGGGUGCgAuuagcGCGGCAGGa -3' miRNA: 3'- gCUGUA--UGU-CCCGCGgUu----CGCUGUCU- -5' |
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| 576 | 3' | -54.7 | AC_000015.1 | + | 15219 | 0.69 | 0.415629 |
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Target: 5'- uGACGgugguaaUGguGGGCGCCG-GCgGACGGAu -3' miRNA: 3'- gCUGU-------AUguCCCGCGGUuCG-CUGUCU- -5' |
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| 576 | 3' | -54.7 | AC_000015.1 | + | 8435 | 0.7 | 0.351685 |
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Target: 5'- -aGCGgugACGGGgacgcGCGCCGGGCGGCAGc -3' miRNA: 3'- gcUGUa--UGUCC-----CGCGGUUCGCUGUCu -5' |
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| 576 | 3' | -54.7 | AC_000015.1 | + | 15772 | 0.79 | 0.101279 |
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Target: 5'- aGACGUGCAgcuucGGGCGCCAGcGCcGGCAGGu -3' miRNA: 3'- gCUGUAUGU-----CCCGCGGUU-CG-CUGUCU- -5' |
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| 576 | 3' | -54.7 | AC_000015.1 | + | 5337 | 1.1 | 0.000554 |
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Target: 5'- cCGACAUACAGGGCGCCAAGCGACAGAa -3' miRNA: 3'- -GCUGUAUGUCCCGCGGUUCGCUGUCU- -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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