Aligned reads window, in color means quality and tags color mode. The top line gives the contig sequence, and below it are the read sequences for the top strand (right-pointing arrows) and bottom strand (left-pointing arrows). Read names are in yellow. The background gray scale indicates base quality, with the highest quality being white and the lowest quality black. Red indicates a character (such as the x or *) that disagrees with the contig sequence. (x) A base that has been masked by cross-match as being vector. (*) A pad that is inserted by phrap to align reads that have insertions and deletions. Tags are indicated by colored bars covering the bottom half of the background square for each base. The blue tag represents sequencing vector, and the orange tag indicates compressions. An edited base has a green tag attached. Gray letters on a black background indicate that phrap clipped these bases off because of low quality.