The chain format describes a pairwise alignment which can allow gaps in both sequences simultaneously. It is deliberately quite dense. Here's a section of a file: chain 4900 chrY 58368225 + 25985403 25985638 chr5 151006098 - 43257292 43257528 1 9 1 0 10 0 5 61 4 0 16 0 4 42 3 0 16 0 8 14 1 0 3 7 0 48 chain 4900 chrY 58368225 + 25985406 25985566 chr5 151006098 - 43549808 43549970 2 16 0 2 60 4 0 10 0 4 70 The chains start with a header line that starts with the word 'chain' and end with a blank line. The lines after the header contain the size of the ungapped alignment, the difference between the end of this block and the beginning of the next block in the human side (dt), and the difference in the mouse side (dq). The last line contains only the ungapped alignment size of the last block. The header line contains the chain score, the human chromosome, chromosome size, strand, and chain extents, the mouse chromosome, chromosome size, strand and chain extents, and the chain id number. The extents are as zero-based half open intervals, meaning the first 100 bases of a sequence are represented as 0 100, while the next 100 bases are represented as 100 200. When the strand is '-' the coordinates are in terms of the reverse-complemented sequence.