Parameters for files in ../Athal/20_BAP_out_t10:
  _sc  score_cutoff    bit score cutoff before diag search 500 
  _cf  compress_factor original matrix is compressed by    25 
  _l   min_diag_len    min diag length of compressed diag  5 
  _sn  sensitivity     sensitivity (see manpage)           75 
  _q   min_diag_qual   min diag quality (see manpage)      9 
       file            input matrix                        chr1x1.hits 
       scale_factor    scales the dot plot                 0.25 
  
  Color key:
       red     both genes are w/w or c/c orientation (or if no w/c info)
       violet  both genes are w/c or c/w orientation
       black   (small plot): diagonal
       green   (large plot): diagonal (numbered to match text output
               in .coords and diagonal_group_*.txt files)
  

  file_list:  [chr1x1.hits]  [chr2x1.hits]  [chr2x2.hits]  [chr3x1.hits]  [chr3x2.hits]  [chr3x3.hits]  [chr4x1.hits]  [chr4x2.hits]  [chr4x3.hits]  [chr4x4.hits]  [chr5x1.hits]  [chr5x2.hits]  [chr5x3.hits]  [chr5x4.hits]  [chr5x5.hits]  
  base_dir:  ../Athal
  in_subdir:  20_BAP_out_t10
  out_subdir:  30_DH_out
  compress_factor:  25
  use_orientation:  1
  make_images:  1
  scale_factor:  0.25
  ids_on_png:  1
  score_column:  7
  score_cutoff:  500
  near_main_diag:  35
  min_diag_len:  5
  sensitivity:  75
  min_diag_qual:  9
  debug:  1


Program: 30_DiagHunter
Version: 1.15
The program was run on 6/17/2003