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Yes there is. Some alleles are closer together and less likely to separate than other alleles. This is typically referred to as linkage.

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Q: Is there a greater chance of crossing over between some pairs of alleles than between others?
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Why does the law of independent assortment relates to crossing over and genetic linkage by?

This recombination of genes, called the crossing over of DNA, can cause alleles previously on the same chromosome to be separated and end up in different daughter cells. The farther the two alleles are apart, the greater the chance that a cross-over event may occur between them, and the greater the chance that the alleles are separated. - See more at: http://www.chacha.com/question/if-mendel's-law-of-independent-assortment-states-that-allele-pairs-separate-independently-of-each-other-during-meiosis.-how-does-this-law-relate-to-crossing-over-and-genetic-linkage#sthash.pJkZU4x9.dpuf


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