miRNA: 3'- -GGGAGGaGCGaccaccACGGUUGGGU- -5'
miRNA: 3'- -GGGAGGAGCGA--------CCa--CCaCGGuUGGGU- -5'
miRNA: 3'- -GGGa-GGAGCGaCCaCCa------------CGGUUGGGU- -5'
miRNA: 3'- -GGgAGGag-CGACCACCA---------CGGU--UGGGU- -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 | |||||||
| 30903 | 3' | -59.6 | NC_006552.1 | + | 32059 | 0.66 | 0.513014 |
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Target: 5'- gCCCUCCaCGCgcagaaUGCCAGCCCGg -3' miRNA: 3'- -GGGAGGaGCGaccaccACGGUUGGGU- -5' |
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| 30903 | 3' | -59.6 | NC_006552.1 | + | 44991 | 0.68 | 0.42624 |
|
Target: 5'- gCCCUCCUCGCUcucugcucGGccaGG-GCCuGCUCAg -3' miRNA: 3'- -GGGAGGAGCGA--------CCa--CCaCGGuUGGGU- -5' |
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| 30903 | 3' | -59.6 | NC_006552.1 | + | 58341 | 0.68 | 0.422586 |
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Target: 5'- uCCUggCCUCGCgGG-GGcaguuucgccgugGCCAGCCCAa -3' miRNA: 3'- -GGGa-GGAGCGaCCaCCa------------CGGUUGGGU- -5' |
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| 30903 | 3' | -59.6 | NC_006552.1 | + | 15267 | 0.72 | 0.243259 |
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Target: 5'- gCCgUCCgcuGCUGGUGGUcacuacuucGCCAcuGCCCAg -3' miRNA: 3'- -GGgAGGag-CGACCACCA---------CGGU--UGGGU- -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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