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axt alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The axtNet and axtChain alignments are produced by processing the alignment files with additional utilities written by Jim Kent at UCSC.
The following segment from an axt file shows the first 2 sets of alignments of the human assembly (the aligning assembly) to mouse chromosome 19 (the primary assembly).
0 chr19 3001012 3001075 chr11 70568380 70568443 - 3500 TCAGCTCATAAATCACCTCCTGCCACAAGCCTGGCCTGGTCCCAGGAGAGTGTCCAGGCTCAGA TCTGTTCATAAACCACCTGCCATGACAAGCCTGGCCTGTTCCCAAGACAATGTCCAGGCTCAGA chr19 3008279 3008357 chr11 70573976 70574054 - 3900 CACAATCTTCACATTGAGATCCTGAGTTGCTGATCAGAATGGAAGGCTGAGCTAAGATGAGCGACGAGGCAATGTCACA CACAGTCTTCACATTGAGGTACCAAGTTGTGGATCAGAATGGAAAGCTAGGCTATGATGAGGGACAGTGCGCTGTCACA
Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines.
The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields:
0 chr19 3001012 3001075 chr11 70568380 70568443 - 3500
The sequence lines contain the sequence of the primary assembly (line 2) and aligning assembly (line 3) with inserts. Repeats are indicated by lower-case letters.