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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 | |||||||
| 28338 | 3' | -54.4 | NC_005946.1 | + | 41976 | 0.66 | 0.909555 |
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Target: 5'- aGUCUcaAGAGUCCccGGGuGGACccgGGGGUc -3' miRNA: 3'- -CAGAa-UUUCAGGcuCCC-CCUG---UCCCG- -5' |
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| 28338 | 3' | -54.4 | NC_005946.1 | + | 71691 | 0.66 | 0.903172 |
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Target: 5'- ------cAGUCCGAagaGGGcuaccuGGACAGGGUa -3' miRNA: 3'- cagaauuUCAGGCU---CCC------CCUGUCCCG- -5' |
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| 28338 | 3' | -54.4 | NC_005946.1 | + | 24721 | 0.67 | 0.866806 |
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Target: 5'- gGUUUUGGuggauccGGUuuGGGGGGGuu-GGGCc -3' miRNA: 3'- -CAGAAUU-------UCAggCUCCCCCuguCCCG- -5' |
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| 28338 | 3' | -54.4 | NC_005946.1 | + | 14983 | 0.68 | 0.835003 |
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Target: 5'- ------cGGUCCGAccccauguugGaGGGGGCGGGGUa -3' miRNA: 3'- cagaauuUCAGGCU----------C-CCCCUGUCCCG- -5' |
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| 28338 | 3' | -54.4 | NC_005946.1 | + | 72854 | 0.69 | 0.770747 |
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Target: 5'- cUCaacauGG-CCGAGGGGG-CGGGGUu -3' miRNA: 3'- cAGaauu-UCaGGCUCCCCCuGUCCCG- -5' |
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| 28338 | 3' | -54.4 | NC_005946.1 | + | 60286 | 0.7 | 0.720692 |
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Target: 5'- --gUUAAAGUCCGAcGGGGuguuuguCAGGGg -3' miRNA: 3'- cagAAUUUCAGGCUcCCCCu------GUCCCg -5' |
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| 28338 | 3' | -54.4 | NC_005946.1 | + | 97243 | 0.7 | 0.710396 |
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Target: 5'- aGUCUUG----CUGAGGGGGcUGGGGCu -3' miRNA: 3'- -CAGAAUuucaGGCUCCCCCuGUCCCG- -5' |
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| 28338 | 3' | -54.4 | NC_005946.1 | + | 3768 | 1.11 | 0.002015 |
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Target: 5'- aGUCUUAAAGUCCGAGGGGGACAGGGCc -3' miRNA: 3'- -CAGAAUUUCAGGCUCCCCCUGUCCCG- -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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