miRNA: 3'- aGCGGGAGAAGGUccaGG----------UCCuaCCG- -5'
miRNA: 3'- aGcGGGAGAAGgUCCAGGUCCu-ACcg -5'
miRNA: 3'- aGCGG-GAGA----AGGU---------CCAGGUCCuACCG- -5'
miRNA: 3'- -AGCGGGAGaAGGUC-CaGGUC-CUACCG- -5'
miRNA: 3'- -AGCGGGAGAAGGUCCAGGUCCUACCG- -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 | |||||||
| 2505 | 3' | -57.7 | NC_001454.1 | + | 17290 | 0.66 | 0.468459 |
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Target: 5'- gCGCCCUCUUUCAaagCCugcucguacgAGGggGGCu -3' miRNA: 3'- aGCGGGAGAAGGUccaGG----------UCCuaCCG- -5' |
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| 2505 | 3' | -57.7 | NC_001454.1 | + | 19598 | 0.66 | 0.418773 |
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Target: 5'- aCcCCCUCUUUgGGGUCCGGGuuUGa- -3' miRNA: 3'- aGcGGGAGAAGgUCCAGGUCCu-ACcg -5' |
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| 2505 | 3' | -57.7 | NC_001454.1 | + | 11838 | 0.69 | 0.283327 |
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Target: 5'- cCGCCuCUCUcacgUCCGuugucagucGGUCUAGGuUGGCc -3' miRNA: 3'- aGCGG-GAGA----AGGU---------CCAGGUCCuACCG- -5' |
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| 2505 | 3' | -57.7 | NC_001454.1 | + | 10328 | 0.7 | 0.248761 |
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Target: 5'- gUUGCUCUC-UCCGGaG-CCGGcGGUGGCa -3' miRNA: 3'- -AGCGGGAGaAGGUC-CaGGUC-CUACCG- -5' |
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| 2505 | 3' | -57.7 | NC_001454.1 | + | 10429 | 1.11 | 0.000228 |
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Target: 5'- cUCGCCCUCUUCCAGGUCCAGGAUGGCc -3' miRNA: 3'- -AGCGGGAGAAGGUCCAGGUCCUACCG- -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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