miRNA: 3'- -GUGGGU--GAUGGUgg---------CCUCuGGAUAGG- -5'
miRNA: 3'- gUGGg-----UgAUGGUGgCCUCUGGauaGG- -5'
miRNA: 3'- gUGGGugauGGUGGCCUCUGgaUAGG- -5'
miRNA: 3'- -GUGGGUGAUGGUGGCCUCUGGAUAGG- -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 | |||||||
| 31273 | 3' | -54.9 | NC_006563.1 | + | 4055 | 0.66 | 0.224304 |
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Target: 5'- aUACCCAauCUACCAaaauaaagaaaGGAG-CUUAUCCa -3' miRNA: 3'- -GUGGGU--GAUGGUgg---------CCUCuGGAUAGG- -5' |
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| 31273 | 3' | -54.9 | NC_006563.1 | + | 7237 | 0.67 | 0.176249 |
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Target: 5'- aGCCaggugaGgUGCCGCgGGGGACCg--CCa -3' miRNA: 3'- gUGGg-----UgAUGGUGgCCUCUGGauaGG- -5' |
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| 31273 | 3' | -54.9 | NC_006563.1 | + | 3250 | 0.73 | 0.066324 |
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Target: 5'- gACCCu---CCACCGGGGAUggAUCCa -3' miRNA: 3'- gUGGGugauGGUGGCCUCUGgaUAGG- -5' |
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| 31273 | 3' | -54.9 | NC_006563.1 | + | 3182 | 1.12 | 0.000036 |
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Target: 5'- gCACCCACUACCACCGGAGACCUAUCCg -3' miRNA: 3'- -GUGGGUGAUGGUGGCCUCUGGAUAGG- -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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