miRNA: 3'- gGUCC----GGAAGG-------UCCCUCAGGUGacgc -5'
miRNA: 3'- -GGu--CCGGAa----GGU-CCCUCAGGUGa--CGc -5'
miRNA: 3'- -GGuCCGGA--------------AGGUCCCUCAgGUGAC-GC- -5'
miRNA: 3'- -GGUCCGGAAGGUCCCUCAGGUGACGC- -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 | |||||||
| 791 | 5' | -58.6 | NC_000855.1 | + | 7574 | 0.66 | 0.169014 |
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Target: 5'- gCAGGgaauCCUUCUucagaaaGGGGAGUCCACa--- -3' miRNA: 3'- gGUCC----GGAAGG-------UCCCUCAGGUGacgc -5' |
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| 791 | 5' | -58.6 | NC_000855.1 | + | 11097 | 0.67 | 0.150263 |
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Target: 5'- gCCuguGGCCUggcgcCCAcGGGAGUUCACcugGCc -3' miRNA: 3'- -GGu--CCGGAa----GGU-CCCUCAGGUGa--CGc -5' |
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| 791 | 5' | -58.6 | NC_000855.1 | + | 6935 | 0.68 | 0.120178 |
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Target: 5'- aCCuGGCCUugaacgucaccagaUCUGGGGGGU-CACUGgCGg -3' miRNA: 3'- -GGuCCGGA--------------AGGUCCCUCAgGUGAC-GC- -5' |
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| 791 | 5' | -58.6 | NC_000855.1 | + | 1136 | 1.09 | 0.000042 |
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Target: 5'- uCCAGGCCUUCCAGGGAGUCCACUGCGu -3' miRNA: 3'- -GGUCCGGAAGGUCCCUCAGGUGACGC- -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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