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		    	The chain format describes a pairwise alignment that allow
		    	gaps in both sequences simultaneously. 
		    	Each set of chain alignments starts with a header line, 
			contains one or more alignment data lines, and 
			terminates with a blank line. The format is 
			deliberately quite dense.  
			 
			Example:
  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 Header Lines 
			
  chain score tName tSize tStrand tStart tEnd qName qSize qStrand qStart qEnd id 
The initial header line starts with the keyword 
			chain, followed by 11 required attribute values,
			and ending with a blank line. The attributes include: 
			
			score -- chain score
			
			tName -- chromosome (reference sequence)
			
			tSize -- chromosome size (reference sequence)
			
			tStrand -- strand (reference sequence)
			
			tStart -- alignment start position (reference sequence)
			
			tEnd -- alignment end position (reference sequence)
			
			qName -- chromosome (query sequence)
			
			qSize -- chromosome size (query sequence)
			
			qStrand -- strand (query sequence)
			
			qStart -- alignment start position (query sequence) 
			
			qEnd -- alignment end position (query sequence)
			
			id -- chain ID
			 
			The alignment start and end positions are represented
			as zero-based half-open intervals. For example, 
			the first 100 bases of a sequence would be represented 
			with start position = 0 and end position = 100, and the 
			next 100 bases would be represented as 
		  	start position = 100 and end position = 200.
			When the strand value is "-", position 
			coordinates are listed
			in terms of the reverse-complemented sequence.
			 
			Alignment Data Lines
			 
			Alignment data lines contain three required attribute values:
			
			  size dt dq 
			
			size -- the size of the ungapped alignment
			
			dt -- the difference between the end of this 
			block and the beginning of the next block (reference sequence) 
			
			dq -- the difference between the end of this 
			block and the beginning of the next block (query sequence) 
			 
			NOTE: The last line of the alignment section 
			contains only one number: the ungapped alignment size 
			of the last block.
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