_ID  DictyExper
calibrate  ARRAY{
  {
    contig  JC1a181a10.r1
    db  /gen/links/dicty/gap/Chr1/CHR1_psi21.0
    id  alpha-actinin 3
    mask  0
    target  Chr1
  }
  {
    contig  JC2e76c04.s1
    ctgorient  +
    ctgrange  JC2c151b02.r1..JC2c121c03.r1 (50000)
    db  /gen/links/dicty/gap/Chr2/CHR2_psi9.0
    id  gpaB
    mask  0
    target  Chr2
  }
  {
    contig  JC2e19h08.s1
    ctgorient  +
    ctgrange  JC2b45c01.s1..JC2a45e08.r1 (66000)
    db  /gen/links/dicty/gap/Chr2/CHR2_psi13.0
    id  myoD
    mask  0
    target  Chr2
  }
  {
    contig  JC2f04b05.r1
    db  /gen/links/dicty/gap/Chr3/CHR3_psi31.0
    id  cprD
    mask  0
    target  Chr3
  }
  {
    contig  JC2c120b07.r1
    ctgorient  +
    ctgrange  JC2a91f06.r1..JC2e69a08.r1
    db  /gen/links/dicty/gap/Chr3/CHR3_psi33.0
    id  dlaA
    mask  0
    target  Chr3
  }
  {
    contig  JAX4a55a02.r1
    ctgorient  +
    ctgrange  -
    db  /gen/links/dicty/gap/Chr3/CHR3_psi30.0
    id  wdpA
    mask  0
    target  Chr3
  }
  {
    contig  sdi45A92g06.q1c
    db  /gen/links/dicty/gap/ChrX/CHRX_psi1.0
    id  comitin
    mask  0
    target  Chr45
    target2  Chr5
  }
  {
    contig  JAX4a84f08.s1
    db  /gen/links/dicty/gap/ChrX/CHRX_psi1.0
    id  cprA
    mask  0
    target  Chr45
    target2  Chr5
  }
  {
    contig  13540a03f03.s1
    db  /gen/links/dicty/gap/DY3850/DY3850.0
    id  DY3850
    mask  12330
    target  Chr6
  }
}
LibGroup  {
  # remember to register new libraries in the substructure "LibGroupRegard"
  JAX4  {
    CloneSelectID  ^JAX4[a-m]
    NtSelectID  ^JAX4.+\.[rst]1$
    NumClone  28437
    NumNt  18204134
    NumRead  48564
    NumSource  /gen/links/dicty/DictyDB/dicty.JAX4
    NumTime  1086071753
    NumTimeOutdate  7620000
    ReadSelectID  ^JAX4.+\.[rst]1$
    SpecificClone  {
      mtDNA  0.01529177
      rDNA  0.06805856
    }
    SpecificRead  {
      mtDNA  0.0173
      rDNA  0.0756
    }
    SpecificTime  1042797321
  }
  # remember to register new libraries in the substructure "LibGroupRegard"
  JC1  {
    CloneSelectID  ^JC1[a-m]
    NtSelectID  ^JC1.+\.[rs]1$
    NumClone  75503
    NumNt  49874613
    NumRead  129864
    NumSource  /gen/links/dicty/DictyDB/dicty.JC1
    NumTime  1089714750
    NumTimeOutdate  7620000
    ReadSelectID  ^JC1.+\.[rs]1$
    SpecificClone  {
      Chr1  0.49297494
      mtDNA  0.00265921
      rDNA  0.01139092
    }
    SpecificRead  {
      Chr1  0.59854083
      Chr2  0.07289252
      Chr3  0.03797480
      Chr45  0.08267347
      Chr6  0.05029589
      mtDNA  0.0025
      NONE  0.1417
      rDNA  0.0133
    }
    SpecificTime  1043772616
  }
  # remember to register new libraries in the substructure "LibGroupRegard"
  JC3  {
    CloneSelectID  ^JC3[a-m]
    NtSelectID  ^JC3.+\.[rs]1$
    NumClone  56947
    NumNt  38747114
    NumRead  100782
    NumSource  /gen/links/dicty/DictyDB/dicty.pre
    NumTime  1088874518
    NumTimeOutdate  5080000
    ReadSelectID  ^JC3.+\.[rs]1$
    SpecificClone  {
      Chr3  0.48993644
      mtDNA  0.00759181
      rDNA  0.01253531
    }
    SpecificRead  {
      Chr1  0.03573758
      Chr2  0.13835006
      Chr3  0.40590370
      Chr45  0.25829757
      Chr6  0.01428949
      mtDNA  0.0076
      NONE  0.1230
      rDNA  0.0165
    }
    SpecificTime  1043337740
  }
  # remember to register new libraries in the substructure "LibGroupRegard"
  sdi45  {
    CloneSelectID  ^(IIC|sdi45)
    NtSelectID  ^(IIC|sdi45)
    NumClone  167379
    NumNt  70608101
    NumRead  225705
    NumSource  /gen/links/dicty/DictyDB/dicty.pre
    NumTime  1090092581
    NumTimeOutdate  2540000
    ReadLen  300
    ReadSelectID  ^(IIC|sdi45)
    SpecificRead  {
      Chr1  0.08224109
      Chr2  0.13918711
      Chr3  0.09170580
      Chr45  0.52929469
      Chr6  0.03596268
      mtDNA  0.0040
      NONE  0.1050
      rDNA  0.0124
    }
    SpecificTime  1043772616
  }
}
# these lists contain the libraries to be considered in certain analyses
# Always enter a library here, if you want to see any effect!
LibGroupRegard  {
  cluster  ARRAY{
    JAX4
    JC3
  }
  probab  ARRAY{
    JAX4
    JC1
    JC3
    sdi45
  }
}
target  {
  Chr1  {
    id  Chr1
    NumNt  4950000
  }
  Chr2  {
    id  Chr2
    NumNt  8270000
  }
  Chr3  {
    id  Chr3
    NumNt  6050000
  }
  Chr45  {
    id  Chr45
    NumNt  10690000
  }
  Chr6  {
    id  Chr6
    NumNt  4030000
  }
  mtDNA  {
    id  mtDNA
    NumNt  55000
  }
  rDNA  {
    id  rDNA
    NumNt  80000
  }
}
TgtGroup  {
  contam  {
    id  contam
    target  ARRAY{
      mtDNA
      rDNA
      NONE
    }
  }
  genome  {
    id  genome
    target  ARRAY{
      Chr1
      Chr2
      Chr3
      Chr45
      Chr6
    }
  }
}
