miRNA: 3'- gGCGGUCG-------CGGUA---------CCGUGUGUGGCGg -5'
miRNA: 3'- -GGCgGUCgCG-GUACcgUGUGUGG---CGG- -5'
miRNA: 3'- gGCGGUCg---CGGUACCGu------GUGUGG--CGG- -5'
miRNA: 3'- -GgCGguCGCGGUACCGUGugUGgCGG- -5'
miRNA: 3'- -GGCGGUCGCGGUACCGUGUGUGGCGG- -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 | |||||||
| 14983 | 3' | -60.1 | NC_003690.1 | + | 3911 | 0.67 | 0.116416 |
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Target: 5'- gCGCUGGCgauggggGCCAUcaucuucagGGCAUGCACUGCa -3' miRNA: 3'- gGCGGUCG-------CGGUA---------CCGUGUGUGGCGg -5' |
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| 14983 | 3' | -60.1 | NC_003690.1 | + | 4903 | 0.68 | 0.097074 |
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Target: 5'- cCCGgCAGgGCaCAUGaaACACACCaauGCCa -3' miRNA: 3'- -GGCgGUCgCG-GUACcgUGUGUGG---CGG- -5' |
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| 14983 | 3' | -60.1 | NC_003690.1 | + | 6254 | 0.69 | 0.07566 |
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Target: 5'- aUGCCAGgccaGCCAUGGUgugaaauCACACUgaGCCa -3' miRNA: 3'- gGCGGUCg---CGGUACCGu------GUGUGG--CGG- -5' |
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| 14983 | 3' | -60.1 | NC_003690.1 | + | 4279 | 0.76 | 0.019813 |
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Target: 5'- gCgGUguGUGCCAUGGCGCugGCgGCUu -3' miRNA: 3'- -GgCGguCGCGGUACCGUGugUGgCGG- -5' |
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| 14983 | 3' | -60.1 | NC_003690.1 | + | 4314 | 1.12 | 1.6e-05 |
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Target: 5'- gCCGCCAGCGCCAUGGCACACACCGCCu -3' miRNA: 3'- -GGCGGUCGCGGUACCGUGUGUGGCGG- -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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