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miRNA: 3'- cAGGCCAGUUGgaCCCGu---UGGUCCUc -5'
miRNA: 3'- cAGGCcaGUUGG---ACCCGUUgGUCCUC- -5'
miRNA: 3'- -CAGG-CCAGUUGGaCCCGU---------------UGGUCCuc -5'
miRNA: 3'- caGGCCaGUUGGACCCGUuggUCCUc -5'
miRNA: 3'- -CAGGCCAGUUGGACCCGUUGGUCCUC- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 8825 | 3' | -57.4 | NC_002484.1 | + | 10262 | 0.66 | 0.564257 |
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Target: 5'- aUCUGGUCGGCa-GGGUugccACCGGGGu -3' miRNA: 3'- cAGGCCAGUUGgaCCCGu---UGGUCCUc -5' |
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| 8825 | 3' | -57.4 | NC_002484.1 | + | 31362 | 0.66 | 0.585785 |
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Target: 5'- cUCCG--CAACCugcUGGGCGAaCAGGAGg -3' miRNA: 3'- cAGGCcaGUUGG---ACCCGUUgGUCCUC- -5' |
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| 8825 | 3' | -57.4 | NC_002484.1 | + | 25828 | 0.66 | 0.600948 |
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Target: 5'- gGUCCuGGUUAGCCgGGGUGaagccgcccuucagcGCCAGGc- -3' miRNA: 3'- -CAGG-CCAGUUGGaCCCGU---------------UGGUCCuc -5' |
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| 8825 | 3' | -57.4 | NC_002484.1 | + | 37388 | 0.66 | 0.607464 |
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Target: 5'- -gCUGGaCAACCUGGGCA---AGGAa -3' miRNA: 3'- caGGCCaGUUGGACCCGUuggUCCUc -5' |
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| 8825 | 3' | -57.4 | NC_002484.1 | + | 19040 | 1.09 | 0.000571 |
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Target: 5'- cGUCCGGUCAACCUGGGCAACCAGGAGg -3' miRNA: 3'- -CAGGCCAGUUGGACCCGUUGGUCCUC- -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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