GDSV and GSV then read in the locations of similarities from this file and creates the graphic images seen in your browser. Similarities that fit the given criteria are shown as diagonal lines indicating the location on each chromosome where the match occurred. Even if a similarity contains mismatches, insertions or deletions, it will still appear as an uninterrupted solid line in the viewer. Therefore, while the length of similarity seen in the view might indicate a region of pure similarity, it may also contain up to the specified number of mismatches plus the specified number of insertions or deletions. See Table 1 for the exact number.
Blue lines indicate direct repeats and green lines indicate inverted repeats.