miRNA: 3'- cGGUAUCGGUga---G-GUugCG-GUUGUCG- -5'
miRNA: 3'- -CGGUa---UCGGuGA--GGUUGCGGUUg-UCG- -5'
miRNA: 3'- -CGGUAUcGGUGA-GGUuGCGGUUGUCG- -5'
miRNA: 3'- -CGGUAUCGGUGAGGUUGCGGUUGUCG- -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 | |||||||
| 4088 | 5' | -52.8 | NC_001655.1 | + | 1818 | 0.67 | 0.272931 |
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Target: 5'- aCCAUGGCUAacaacCgCAugGCaCAACGGCu -3' miRNA: 3'- cGGUAUCGGUga---G-GUugCG-GUUGUCG- -5' |
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| 4088 | 5' | -52.8 | NC_001655.1 | + | 8759 | 0.68 | 0.214129 |
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Target: 5'- aGCCAgggcGGUC-CUcgCCAGCGCCAAgaGGCg -3' miRNA: 3'- -CGGUa---UCGGuGA--GGUUGCGGUUg-UCG- -5' |
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| 4088 | 5' | -52.8 | NC_001655.1 | + | 3337 | 0.76 | 0.059762 |
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Target: 5'- aGUCAUGaCCACUgCCAuCGCUGACAGCg -3' miRNA: 3'- -CGGUAUcGGUGA-GGUuGCGGUUGUCG- -5' |
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| 4088 | 5' | -52.8 | NC_001655.1 | + | 5174 | 1.15 | 0.000043 |
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Target: 5'- aGCCAUAGCCACUCCAACGCCAACAGCg -3' miRNA: 3'- -CGGUAUCGGUGAGGUUGCGGUUGUCG- -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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