miRNA: 3'- caGUGUUGG--UCCUCGCCaACAUgGca -5'
miRNA: 3'- caGU-GUUGGUCC-UCGCCAACaUGgCA- -5'
miRNA: 3'- caGUGUUGGUCCU---------CGCCAACau--GGCa -5'
miRNA: 3'- -CAGUGUUGGUCCUCGCCAACAUGGCA- -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 | |||||||
| 2523 | 5' | -53.6 | NC_001454.1 | + | 29068 | 0.67 | 0.601168 |
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Target: 5'- -aCACAGCUauAGGAGCGGaUGUGgCu- -3' miRNA: 3'- caGUGUUGG--UCCUCGCCaACAUgGca -5' |
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| 2523 | 5' | -53.6 | NC_001454.1 | + | 646 | 0.68 | 0.544031 |
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Target: 5'- -aCGcCAACCAGGaAGCGGUUG-AUgGUa -3' miRNA: 3'- caGU-GUUGGUCC-UCGCCAACaUGgCA- -5' |
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| 2523 | 5' | -53.6 | NC_001454.1 | + | 6017 | 0.68 | 0.544031 |
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Target: 5'- -gCACAACCGGGGcuggcauguGCGGUUGcuucCCGa -3' miRNA: 3'- caGUGUUGGUCCU---------CGCCAACau--GGCa -5' |
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| 2523 | 5' | -53.6 | NC_001454.1 | + | 20907 | 1.07 | 0.001023 |
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Target: 5'- cGUCACAACCAGGAGCGGUUGUACCGUu -3' miRNA: 3'- -CAGUGUUGGUCCUCGCCAACAUGGCA- -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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