Figure 3. Dot matrix analysis illustrating direct (A) and inverted (B) repeats.

Figure 3

Dot matrix analysis illustrating direct (A) and inverted (B) repeats. The main diagonal in A is the identity diagonal; the shorter, parallel lines are manifestations of the direct repeats, of which the shortest are simple repeats of the letter E. This illustration was hand-executed with word size of 1. (B) When the HIV-2 TAR sequence is compared by a computer to itself, scoring complementary bases as matches (color), inverted repeats, manifested by lines normal to the main diagonal, become apparent over the 3′stretch of the sequence (see Figs. 4 and 7). In the latter analysis, the word size was 1, the window size was 15, and the cutoff value was 65%.

From: Retroviral Sequences

Cover of Retroviruses
Retroviruses.
Coffin JM, Hughes SH, Varmus HE, editors.
Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 1997.
Copyright © 1997, Cold Spring Harbor Laboratory Press.

NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.