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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.
		 Example:The following segment from an axt file shows the first 2 
		sets of alignments of the human assembly (the aligning 
		assembly) to mouse chromsome 19 (the primary assembly).
   0 chr19 3001012 3001075 chr11 70568380 70568443 - 3500
  TCAGCTCATAAATCACCTCCTGCCACAAGCCTGGCCTGGTCCCAGGAGAGTGTCCAGGCTCAGA
  TCTGTTCATAAACCACCTGCCATGACAAGCCTGGCCTGTTCCCAAGACAATGTCCAGGCTCAGA
  1 chr19 3008279 3008357 chr11 70573976 70574054 - 3900
  CACAATCTTCACATTGAGATCCTGAGTTGCTGATCAGAATGGAAGGCTGAGCTAAGATGAGCGACGAGGCAATGTCACA
  CACAGTCTTCACATTGAGGTACCAAGTTGTGGATCAGAATGGAAAGCTAGGCTATGATGAGGGACAGTGCGCTGTCACA
		 StructureEach 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.
 1. Summary line
	    	 0 chr19 3001012 3001075 chr11 70568380 70568443 - 3500The summary line contains chromosomal position and size 
		information about the alignment. It consists of 9 required
		fields: 
		
		Alignment number -- The alignment numbering 
		starts with
		0 and increments by 1, i.e. the first alignment in a file
    		is numbered 0,  the next 1, etc. 
		
		Chromosome (primary organism)
		
		Alignment start (primary organism) -- The 
		first base is numbered 1.
		
		Alignment end (primary organism) -- The end 
		base is included.
		
		Chromosome (aligning organism)
		
		Alignment start (aligning organism)
		
		Alignment end (aligning organism)
		
		Strand (aligning organism) -- If the strand 
		value is "-", the values of the aligning organism's 
		start and end fields are relative to the reverse-complemented
    		coordinates of its chromosome.
		
		Blastz score -- Different blastz scoring 
		matrices are used for different organisms. See the README.txt 
		file in the alignments directory for scoring information 
		specific to a pair of alignments.
		 2. & 3. Sequence lines
	    	  TCAGCTCATAAATCACCTCCTGCCACAAGCCTGGCCTGGTCCCAGGAGAGTGTCCAGGCTCAGA
  TCTGTTCATAAACCACCTGCCATGACAAGCCTGGCCTGTTCCCAAGACAATGTCCAGGCTCAGAThe 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. |