miRNA: 3'- -CUGCA-CAAuCGgCUUCg------GUCGCGGCU- -5'
miRNA: 3'- cugCACAA--UCGGCUUCGg------------UCGCGGcu -5'
miRNA: 3'- -CUGCACaa-UCG-GCU-UCGGUCGCGGCu -5'
miRNA: 3'- -CUGCACAAUCGGCUUCGGUCGCGGCU- -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 | |||||||
| 12298 | 3' | -56.2 | NC_003313.1 | + | 19132 | 0.67 | 0.411264 |
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Target: 5'- uGACGUcGUU-GUgGAAGaugaagaCAGCGCCGAa -3' miRNA: 3'- -CUGCA-CAAuCGgCUUCg------GUCGCGGCU- -5' |
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| 12298 | 3' | -56.2 | NC_003313.1 | + | 16970 | 0.68 | 0.379201 |
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Target: 5'- --gGUGUUucAGCCGAAGCagauacagacccaAGCGCCa- -3' miRNA: 3'- cugCACAA--UCGGCUUCGg------------UCGCGGcu -5' |
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| 12298 | 3' | -56.2 | NC_003313.1 | + | 24049 | 0.72 | 0.199299 |
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Target: 5'- aGAUGUGgcaGGCaUGAcGGCCAGCGCCGu -3' miRNA: 3'- -CUGCACaa-UCG-GCU-UCGGUCGCGGCu -5' |
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| 12298 | 3' | -56.2 | NC_003313.1 | + | 20113 | 1.09 | 0.000409 |
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Target: 5'- uGACGUGUUAGCCGAAGCCAGCGCCGAa -3' miRNA: 3'- -CUGCACAAUCGGCUUCGGUCGCGGCU- -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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