When paired sequences are imported, the sequence list created is marked as containing paired data. This can be seen in the Element info view and can be edited within that view (Element information).
A sequence lists can contain single end reads or it can contain paired end reads. A given list cannot contain a mixture of these.
The most common way that paired sequence lists are created is when importing NGS sequence data, as described in Import high-throughput sequencing data. See handling paired data for more information about handling paired data after import.
To create a paired sequence list from existing sequence lists, for example by merging lists, the input lists must be marked as paired and must have the same distance settings. If the input lists do not meet these criteria, a message is shown warning that the resulting sequence list will be unpaired (figure 15.6).