miRNA: 3'- gaaCCgGGACGa---CGUCGGGgaCGCGc -5'
miRNA: 3'- gaACCg--GGaCGACGUCGGgGAC-GCGC- -5'
miRNA: 3'- gaaCCG-GG--ACGACg-------UCGGGGACGCGC- -5'
miRNA: 3'- -GAACCGGGACGACGUCGGGGACGCGC- -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 | |||||||
| 2504 | 3' | -62.8 | NC_001454.1 | + | 11291 | 0.66 | 0.213445 |
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Target: 5'- --cGGaCCUGCaaugGCAGCCCa-GCGCc -3' miRNA: 3'- gaaCCgGGACGa---CGUCGGGgaCGCGc -5' |
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| 2504 | 3' | -62.8 | NC_001454.1 | + | 3397 | 0.67 | 0.17691 |
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Target: 5'- -gUGGauaCC-GCUGCAGCUgCUGcCGCGu -3' miRNA: 3'- gaACCg--GGaCGACGUCGGgGAC-GCGC- -5' |
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| 2504 | 3' | -62.8 | NC_001454.1 | + | 6085 | 0.72 | 0.078448 |
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Target: 5'- --gGGCgCCuuUGCUGgaccaaugAGCCCCUGCGCGg -3' miRNA: 3'- gaaCCG-GG--ACGACg-------UCGGGGACGCGC- -5' |
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| 2504 | 3' | -62.8 | NC_001454.1 | + | 9577 | 1.09 | 0.000076 |
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Target: 5'- aCUUGGCCCUGCUGCAGCCCCUGCGCGg -3' miRNA: 3'- -GAACCGGGACGACGUCGGGGACGCGC- -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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