miRNA: 3'- guCCUACGGCaCACA----CUCaaGUAGCG- -5'
miRNA: 3'- gUCCuaCGGCa---CAC-ACu-CAAGUAGCG- -5'
miRNA: 3'- -GUCCU------------ACGGCACacaCUCaAGUAGCG- -5'
miRNA: 3'- gUCCUACGGCACaCACuCaa--GUa--GCG- -5'
miRNA: 3'- -GUCCUACGGCACACACUCAAGUAGCG- -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 | |||||||
| 5156 | 3' | -51.5 | NC_001798.1 | + | 104573 | 0.66 | 0.99239 |
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Target: 5'- -cGGGUGCUG-GUGUcucgGGGaaCGUCGCc -3' miRNA: 3'- guCCUACGGCaCACA----CUCaaGUAGCG- -5' |
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| 5156 | 3' | -51.5 | NC_001798.1 | + | 46971 | 0.66 | 0.985414 |
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Target: 5'- uGGGccGCUGggugGUGcUGuuGUUCGUCGCg -3' miRNA: 3'- gUCCuaCGGCa---CAC-ACu-CAAGUAGCG- -5' |
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| 5156 | 3' | -51.5 | NC_001798.1 | + | 126679 | 0.68 | 0.96857 |
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Target: 5'- cCGGGAaaaagagugguuUGCCGUG---GAGcUCGUCGCg -3' miRNA: 3'- -GUCCU------------ACGGCACacaCUCaAGUAGCG- -5' |
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| 5156 | 3' | -51.5 | NC_001798.1 | + | 36293 | 0.72 | 0.857968 |
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Target: 5'- gGGGGUGCCGUGgGUGuGgcggCGgggCGCg -3' miRNA: 3'- gUCCUACGGCACaCACuCaa--GUa--GCG- -5' |
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| 5156 | 3' | -51.5 | NC_001798.1 | + | 117597 | 1.11 | 0.005824 |
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Target: 5'- gCAGGAUGCCGUGUGUGAGUUCAUCGCc -3' miRNA: 3'- -GUCCUACGGCACACACUCAAGUAGCG- -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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