miRNA: 3'- -GCGGGaauu------UCGCgaCCAGGCAgucu -5'
miRNA: 3'- gCGGGa-AUUUC--GCGA-CCa----GGCAGUCU- -5'
miRNA: 3'- gCGGGaauuuCGCGa--CCAGGC--AGUCu -5'
miRNA: 3'- -GCGGGAAuuUCG--------CGACCAGgCAGUCu -5'
miRNA: 3'- -GCGGGAAUUUCGCGACCAGGCAGUCU- -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 | |||||||
| 22602 | 3' | -54.4 | NC_005091.1 | + | 11448 | 0.66 | 0.779299 |
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Target: 5'- aCGCCCggacucaaacAGCGgaGGUCCGUg--- -3' miRNA: 3'- -GCGGGaauu------UCGCgaCCAGGCAgucu -5' |
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| 22602 | 3' | -54.4 | NC_005091.1 | + | 48631 | 0.66 | 0.773255 |
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Target: 5'- gGCCCgaUGAGGauCGCUcGGggcggCCGUCGGGg -3' miRNA: 3'- gCGGGa-AUUUC--GCGA-CCa----GGCAGUCU- -5' |
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| 22602 | 3' | -54.4 | NC_005091.1 | + | 55207 | 0.67 | 0.688588 |
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Target: 5'- gGCCCgu---GCGCgggGGUCCGgcUCGGu -3' miRNA: 3'- gCGGGaauuuCGCGa--CCAGGC--AGUCu -5' |
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| 22602 | 3' | -54.4 | NC_005091.1 | + | 22448 | 0.7 | 0.524357 |
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Target: 5'- cCGCCUUUcgGGUcaucugcgGCUGGUCgGUCAGc -3' miRNA: 3'- -GCGGGAAuuUCG--------CGACCAGgCAGUCu -5' |
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| 22602 | 3' | -54.4 | NC_005091.1 | + | 30167 | 1.09 | 0.001265 |
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Target: 5'- cCGCCCUUAAAGCGCUGGUCCGUCAGAc -3' miRNA: 3'- -GCGGGAAUUUCGCGACCAGGCAGUCU- -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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