Note on counting crossovers:

Note that, experimentally, crossovers are only observable if they occur in a region that will produce a distinct daughter sequence. One crossover between a consecutive pair of variable positions will produce the same daughter sequence as 3, 5, 7, ... crossovers. Similarly 2, 4, 6, ... crossovers produce the same daughter sequence as no crossovers at all. In addition, any crossovers occurring between one end of the sequence and the first variable position are also unable to be detected by analysis of the daughter sequence.

Typically you will find the mean number of observable crossovers by sequence analysis of a sample of daughter sequences. Nonetheless, the underlying true number of crossovers is also an important statistic to know - especially when you want to try and vary the crossover rate by making adjustments to your recombination protocol.

In DRIVeR, you can choose to enter either the mean number of observable crossovers or the true mean number of all crossovers. Either way, DRIVeR will also calculate and tell you the other statistic.

Note also the following:

• The maximum observable crossover rate is (M-1)/2, where M is the number of variable positions. If the true crossover rate is very high, then the variable positions will be essentially randomly assigned in each daughter sequence, and all possible daughters will be essentially equally likely (in fact you can use GLUE instead of DRIVeR).
  
  
• Since we assume that crossovers cannot occur immediately following a variable position (due to the nature of the reassembly reaction), if two variable positions are adjacent in the parent sequences, then they will remain linked in all daughter sequences and the number of possible daughter sequences and maximum observable crossover rate will be reduced accordingly.
  
  

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