Window Alignment detects alternative assemblies. Displayed is a part of the temporary BAC assembly by the Medicago sequencing consortium drawn to scale using + and - signs to indicate sequence strand. Five BACs (black boxes) are arranged into two assemblies separated by a 60 kbp gap of unknown sequence. However, a long exact match of AC148343+ with AC150776+ suggests another possible assembly indicated by white boxes. See Table 4 for the match quality of all considered overlaps.