miRNA: 3'- -GCGGCGGGgagaGCgGGUCGaCGgCG- -5'
miRNA: 3'- gCGGCGg---GGagaGCGGgUCGa-CGGCG- -5'
miRNA: 3'- -GCGGCGG-GGAGaGCgGGUCGa--CGGCG- -5'
miRNA: 3'- -GCGGCGG-GGAGaGC-GGGUCGa-CGGCG- -5'
miRNA: 3'- -GCGGCGGGGAGAGCGGGUCGACGGCG- -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 | |||||||
| 2203 | 5' | -65.2 | NC_001402.1 | + | 1335 | 0.67 | 0.007985 |
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Target: 5'- gCGCCGCCCa---CGgCCGGCgGCgGCu -3' miRNA: 3'- -GCGGCGGGgagaGCgGGUCGaCGgCG- -5' |
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| 2203 | 5' | -65.2 | NC_001402.1 | + | 1321 | 0.68 | 0.007176 |
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Target: 5'- aGCCGCggggCCgg-CGCCgGGCggGCCGCg -3' miRNA: 3'- gCGGCGg---GGagaGCGGgUCGa-CGGCG- -5' |
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| 2203 | 5' | -65.2 | NC_001402.1 | + | 1173 | 0.74 | 0.001661 |
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Target: 5'- cCGCCGCCuCCUCcCG-CCGGCcccGCCGCc -3' miRNA: 3'- -GCGGCGG-GGAGaGCgGGUCGa--CGGCG- -5' |
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| 2203 | 5' | -65.2 | NC_001402.1 | + | 1135 | 0.8 | 0.000412 |
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Target: 5'- cCGCCGCCgCCUCcCGaCCCGGCccGCCGCc -3' miRNA: 3'- -GCGGCGG-GGAGaGC-GGGUCGa-CGGCG- -5' |
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| 2203 | 5' | -65.2 | NC_001402.1 | + | 868 | 1.1 | 0 |
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Target: 5'- gCGCCGCCCCUCUCGCCCAGCUGCCGCu -3' miRNA: 3'- -GCGGCGGGGAGAGCGGGUCGACGGCG- -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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