miRNA: 3'- -GGG---CCGuGGG-GUAGaaaUGGUAGGCG- -5'
miRNA: 3'- -GGGCCGu---GGGGUaga-----AAUGG-------UAGGCG- -5'
miRNA: 3'- -GGGC------CGUGGg--GUAGaa---AUGGUAGGCG- -5'
miRNA: 3'- -GGGCCGUGGGGUAGAAAUGGUAGGCG- -5'
miRNA: 3'- -GGGCCGUGGGGUAGAAAUGGUAGGCG- -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 | |||||||
| 33182 | 5' | -54.7 | NC_007501.1 | + | 16589 | 0.67 | 0.612615 |
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Target: 5'- aCCUuugGGC-CCCaCAUC---ACCGUCUGCg -3' miRNA: 3'- -GGG---CCGuGGG-GUAGaaaUGGUAGGCG- -5' |
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| 33182 | 5' | -54.7 | NC_007501.1 | + | 13374 | 0.67 | 0.577843 |
|
Target: 5'- aUCCGGCucauCCCCAaaaauuagUUGCUgugguucGUCCGCa -3' miRNA: 3'- -GGGCCGu---GGGGUaga-----AAUGG-------UAGGCG- -5' |
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| 33182 | 5' | -54.7 | NC_007501.1 | + | 35728 | 0.68 | 0.523896 |
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Target: 5'- aCCCGcaagucGCACCauuCGUCaugugUGCCGUCUGCu -3' miRNA: 3'- -GGGC------CGUGGg--GUAGaa---AUGGUAGGCG- -5' |
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| 33182 | 5' | -54.7 | NC_007501.1 | + | 17033 | 1.14 | 0.000309 |
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Target: 5'- cCCCGGCACCCCAUCUUUACCAUCCGCa -3' miRNA: 3'- -GGGCCGUGGGGUAGAAAUGGUAGGCG- -5' |
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| 33182 | 5' | -54.7 | NC_007501.1 | + | 16820 | 1.14 | 0.000309 |
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Target: 5'- cCCCGGCACCCCAUCUUUACCAUCCGCa -3' miRNA: 3'- -GGGCCGUGGGGUAGAAAUGGUAGGCG- -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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