miRNA: 3'- -CGGA-GCAGUGCGCcCCCUUAcaCGUu -5'
miRNA: 3'- cGGAGCAGU-GCGCC----CC-CU-UACACGUU- -5'
miRNA: 3'- -CGG--AGCAGUgCGCC-CCCUUACA---------CGUU- -5'
miRNA: 3'- -CGG-------AGCAGUgCGC-CCCCUUa-CACGUU- -5'
miRNA: 3'- -CGGAGCAGUGCGCCCCCUUACACGUU- -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 | |||||||
| 20772 | 3' | -57.2 | NC_004689.1 | + | 36323 | 0.66 | 0.650419 |
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Target: 5'- cGCCUgUGUCACGCG-GGGAAUc-GCGc -3' miRNA: 3'- -CGGA-GCAGUGCGCcCCCUUAcaCGUu -5' |
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| 20772 | 3' | -57.2 | NC_004689.1 | + | 5071 | 0.67 | 0.607387 |
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Target: 5'- cCCUCGUCAuUGCGGacacGGcGAaAUGUGCGAc -3' miRNA: 3'- cGGAGCAGU-GCGCC----CC-CU-UACACGUU- -5' |
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| 20772 | 3' | -57.2 | NC_004689.1 | + | 57726 | 0.68 | 0.533161 |
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Target: 5'- uGCCagUCGUCA-GCGGuGGGGAUGUccugccacgGCAGg -3' miRNA: 3'- -CGG--AGCAGUgCGCC-CCCUUACA---------CGUU- -5' |
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| 20772 | 3' | -57.2 | NC_004689.1 | + | 67661 | 0.71 | 0.369896 |
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Target: 5'- aGCCacgaaugUCGUCAgGUGaGGGGAAcgGUGCAGc -3' miRNA: 3'- -CGG-------AGCAGUgCGC-CCCCUUa-CACGUU- -5' |
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| 20772 | 3' | -57.2 | NC_004689.1 | + | 17677 | 1.07 | 0.001084 |
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Target: 5'- gGCCUCGUCACGCGGGGGAAUGUGCAAc -3' miRNA: 3'- -CGGAGCAGUGCGCCCCCUUACACGUU- -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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