miRNA: 3'- cCACC-----UCGa-AGGGGUAgGGAU---CGC-GG- -5'
miRNA: 3'- -CCACC-UCGaaGGGGUa--GgGAUCGCGg -5'
miRNA: 3'- -CCACCuCGaag--GGGUAGGgaUCGCGG- -5'
miRNA: 3'- -CCaCCUCG--------AAGGGGUAGGGAUCGCGg -5'
miRNA: 3'- -CCACCUCGAAGGGGUAGGGAUCGCGG- -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 | |||||||
| 31603 | 3' | -57.7 | NC_006875.1 | + | 3981 | 0.66 | 0.136185 |
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Target: 5'- uGUGGuccaaGGCcgUCCCCGUgCCUGcccGCGaCCa -3' miRNA: 3'- cCACC-----UCGa-AGGGGUAgGGAU---CGC-GG- -5' |
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| 31603 | 3' | -57.7 | NC_006875.1 | + | 1843 | 0.68 | 0.08957 |
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Target: 5'- aGGUGGuGGCa-CCCCAgggUgCUGGCGCa -3' miRNA: 3'- -CCACC-UCGaaGGGGUa--GgGAUCGCGg -5' |
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| 31603 | 3' | -57.7 | NC_006875.1 | + | 4140 | 0.69 | 0.073577 |
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Target: 5'- aGGUGG-GCguugaCCCAUCC--AGCGCUa -3' miRNA: 3'- -CCACCuCGaag--GGGUAGGgaUCGCGG- -5' |
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| 31603 | 3' | -57.7 | NC_006875.1 | + | 979 | 0.71 | 0.054622 |
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Target: 5'- aGG-GGGGCcgcccgagUUUUCCAUCCCUGGUGUa -3' miRNA: 3'- -CCaCCUCG--------AAGGGGUAGGGAUCGCGg -5' |
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| 31603 | 3' | -57.7 | NC_006875.1 | + | 5866 | 1.14 | 0.000011 |
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Target: 5'- gGGUGGAGCUUCCCCAUCCCUAGCGCCa -3' miRNA: 3'- -CCACCUCGAAGGGGUAGGGAUCGCGG- -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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