We found a tandem repeat sequence in the region (designated BS7) in which restriction fragments HI D and I B overlap each other, near the centre of the unique long sequence (U) of the herpes simplex virus type 1 (HSV-1) strain F genome. The I physical map of BS7 was constructed, and the position of a heterogeneous I subfragment from HSV-1 isolates and plaque-purified clones from a single strain was defined on the map. The maximum size difference in the I subfragment was estimated to be 600 bp between these isolates and 100 bp between the clones. The 0.23 kb I subfragment recloned from BS7 was sequenced, and was shown to contain a tandem repeat sequence consisting of 15 units of 12 bp, 5′ TTGGGGCTGGGG 3′. These results suggest that the fragment length heterogeneity in the U of HSV-1 isolates and clones is attributable to copy number variation of the tandem repeat sequence.


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