miRNA: 3'- aCU--UCGAUGGCGUUAgCuc-CCUCaac -5'
miRNA: 3'- aCUUCGA---UGGCGU------UAGCUCCCuCaac -5'
miRNA: 3'- aCuuCGAU--GGCG--UUAGCUCC-CUCAac -5'
miRNA: 3'- -ACUUCGAUGGCGUUAGCUCCCUCAAC- -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 | |||||||
| 31695 | 5' | -51.4 | NC_006934.1 | + | 4060 | 0.66 | 0.332097 |
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Target: 5'- aGAgcGGCUGCCGCAAUgGcucGGAGg-- -3' miRNA: 3'- aCU--UCGAUGGCGUUAgCuc-CCUCaac -5' |
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| 31695 | 5' | -51.4 | NC_006934.1 | + | 6812 | 0.68 | 0.253683 |
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Target: 5'- gGAGGCUaagACUGCAauuuccAUCGAGGGuGa-- -3' miRNA: 3'- aCUUCGA---UGGCGU------UAGCUCCCuCaac -5' |
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| 31695 | 5' | -51.4 | NC_006934.1 | + | 4350 | 0.68 | 0.238467 |
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Target: 5'- aGggGCUGauCCGUcaGGUCGGGGcGGGUg- -3' miRNA: 3'- aCuuCGAU--GGCG--UUAGCUCC-CUCAac -5' |
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| 31695 | 5' | -51.4 | NC_006934.1 | + | 6175 | 1.1 | 0.00013 |
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Target: 5'- gUGAAGCUACCGCAAUCGAGGGAGUUGg -3' miRNA: 3'- -ACUUCGAUGGCGUUAGCUCCCUCAAC- -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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