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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 | |||||||
| 28560 | 5' | -49.8 | NC_005946.1 | + | 101840 | 0.66 | 0.989554 |
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Target: 5'- uCAGgUUCGAGAGGGUgUacagCGUCAGgUa -3' miRNA: 3'- -GUCgAAGUUCUCUCGgAa---GCAGUUgA- -5' |
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| 28560 | 5' | -49.8 | NC_005946.1 | + | 76220 | 0.67 | 0.977556 |
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Target: 5'- uCAGUcUCAAGAGGGCUcUUGUCcucucgaGACUg -3' miRNA: 3'- -GUCGaAGUUCUCUCGGaAGCAG-------UUGA- -5' |
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| 28560 | 5' | -49.8 | NC_005946.1 | + | 450 | 0.68 | 0.96583 |
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Target: 5'- aGGCUgagCAAGAGGGCCUccauccucCGUCucCUg -3' miRNA: 3'- gUCGAa--GUUCUCUCGGAa-------GCAGuuGA- -5' |
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| 28560 | 5' | -49.8 | NC_005946.1 | + | 60392 | 0.69 | 0.945243 |
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Target: 5'- cCGGCaUCAGGAGGGCagaggCgGUCAGCg -3' miRNA: 3'- -GUCGaAGUUCUCUCGgaa--G-CAGUUGa -5' |
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| 28560 | 5' | -49.8 | NC_005946.1 | + | 86861 | 0.71 | 0.851376 |
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Target: 5'- gAGCagUCAGGGGAGCgUcguugUCGUCGACc -3' miRNA: 3'- gUCGa-AGUUCUCUCGgA-----AGCAGUUGa -5' |
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| 28560 | 5' | -49.8 | NC_005946.1 | + | 44524 | 0.73 | 0.776547 |
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Target: 5'- aGGCgucuUgAGGGGAGCC-UCGUCGACa -3' miRNA: 3'- gUCGa---AgUUCUCUCGGaAGCAGUUGa -5' |
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| 28560 | 5' | -49.8 | NC_005946.1 | + | 77288 | 0.75 | 0.681166 |
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Target: 5'- gAGC-UCGAGGaGGCUUUCGUCGACUu -3' miRNA: 3'- gUCGaAGUUCUcUCGGAAGCAGUUGA- -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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