One end of each bar is coloured light blue. This denotes the end of the contig where the paired reads lie. Above the bars, the number of distinct contig - contig joins that have been found are shown. The actual read pairs are listed, together with their positions within the two contigs. Read names in red correspond to the red contig, read names in blue are those in the blue contig.
Negative numbers are positions counted from the end of the contig in a backwards sense.
Successive pairs have lower scores i.e. a smaller number of read pairs linking them. Scoring Each potential contig - contig join that the program locates is given a score. There may be bugs in this. Basically the higher the score the more faith you can have that there is a join between the 2 contigs. The selection box at the top of the window allows you to select the minimum size of contig to display.