miRNA: 3'- aAGacaCGGGCggCGGUUGG------------GCAGAC- -5'
miRNA: 3'- aagACACGGGC--GGCGGUUG-GGcAGac -5'
miRNA: 3'- -AAGACACGGGCGGCGGU----UGGGcAGAc -5'
miRNA: 3'- aagaCAC-GGG-CGGCGGUUGGGCagac -5'
miRNA: 3'- -AAGACACGGGCGGCGGUUGGGCAGAC- -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 | |||||||
| 22921 | 5' | -60.5 | NC_005137.2 | + | 110570 | 0.66 | 0.665985 |
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Target: 5'- gUCgc-GCCCGuuGCCAGCUgcggaaacaccaCGUCUGu -3' miRNA: 3'- aAGacaCGGGCggCGGUUGG------------GCAGAC- -5' |
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| 22921 | 5' | -60.5 | NC_005137.2 | + | 70586 | 0.67 | 0.605112 |
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Target: 5'- --gUGUGCCCGaaCCGCCAACaCCuUCa- -3' miRNA: 3'- aagACACGGGC--GGCGGUUG-GGcAGac -5' |
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| 22921 | 5' | -60.5 | NC_005137.2 | + | 15141 | 0.68 | 0.544926 |
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Target: 5'- aUUUUGUGUCCGCUGCCAuacaGCUCcUCUu -3' miRNA: 3'- -AAGACACGGGCGGCGGU----UGGGcAGAc -5' |
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| 22921 | 5' | -60.5 | NC_005137.2 | + | 122225 | 0.7 | 0.422966 |
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Target: 5'- ---aGUGaCCCgGCCGCCGACCCGg--- -3' miRNA: 3'- aagaCAC-GGG-CGGCGGUUGGGCagac -5' |
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| 22921 | 5' | -60.5 | NC_005137.2 | + | 19547 | 1.06 | 0.001336 |
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Target: 5'- gUUCUGUGCCCGCCGCCAACCCGUCUGa -3' miRNA: 3'- -AAGACACGGGCGGCGGUUGGGCAGAC- -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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