miRNA: 3'- -UUCuGCA-CAAGAGGgU--UCUGGAGaug -5'
miRNA: 3'- -UUCUGCaCA--------AGa---GGGuuCUGGAGAUG- -5'
miRNA: 3'- -UUCUGCACAAG--AGGGuu--------CUGGAGAUG- -5'
miRNA: 3'- uuCUGCACA-----AGaGGGUUCUgGAGAUG- -5'
miRNA: 3'- -UUCUGCACAAGAGGGUUCUGGAGAUG- -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 | |||||||
| 12606 | 5' | -51.4 | NC_003345.1 | + | 15434 | 0.66 | 0.93393 |
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Target: 5'- gGGGuCGUcGUUCUCCgGguAGACCUCg-- -3' miRNA: 3'- -UUCuGCA-CAAGAGGgU--UCUGGAGaug -5' |
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| 12606 | 5' | -51.4 | NC_003345.1 | + | 56645 | 0.66 | 0.928325 |
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Target: 5'- gGAGGCG-GUuucggcuaUCgaggCCCu-GACCUCUACg -3' miRNA: 3'- -UUCUGCaCA--------AGa---GGGuuCUGGAGAUG- -5' |
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| 12606 | 5' | -51.4 | NC_003345.1 | + | 73120 | 0.69 | 0.802029 |
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Target: 5'- gGGGGCGUGUUCcuUCCCcgugaacuucGGCUUCUGCc -3' miRNA: 3'- -UUCUGCACAAG--AGGGuu--------CUGGAGAUG- -5' |
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| 12606 | 5' | -51.4 | NC_003345.1 | + | 42648 | 0.7 | 0.782161 |
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Target: 5'- -uGGCGUGUagaacUC-CCCGAGAgCUUUGCg -3' miRNA: 3'- uuCUGCACA-----AGaGGGUUCUgGAGAUG- -5' |
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| 12606 | 5' | -51.4 | NC_003345.1 | + | 23675 | 1.09 | 0.003355 |
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Target: 5'- gAAGACGUGUUCUCCCAAGACCUCUACg -3' miRNA: 3'- -UUCUGCACAAGAGGGUUCUGGAGAUG- -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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