Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_6009

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 8775
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32


Found at i:3793 original size:28 final size:28

Alignment explanation


    Indices: 3730--3910  Score: 303
    Period size: 28  Copynumber: 6.5  Consensus size: 28

       3720 ATATTAAGTC

                    *       *           
       3730 CGCACACTCAGTGCTATATAATC-AACT
          1 CGCACACTTAGTGCTACATAATCAAACT

             *              *           
       3757 CACACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTACATAATCAAACT

                                        
       3785 CGCACACTTA-TGCTACATAATCAAACT
          1 CGCACACTTAGTGCTACATAATCAAACT

                                        
       3812 CGCACACTTAGTGCTACATAATCAAACT
          1 CGCACACTTAGTGCTACATAATCAAACT

               *                        
       3840 CGCGCACTTAGTGCTACATAATCAAACT
          1 CGCACACTTAGTGCTACATAATCAAACT

                                        
       3868 CGCACACTTAGTGCTACATAATCAAACT
          1 CGCACACTTAGTGCTACATAATCAAACT

                           
       3896 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       3911 GTACAATTTA


Statistics
Matches: 146,  Mismatches: 6, Indels: 3
        0.94            0.04        0.02

Matches are distributed among these distances:
  27   47  0.32
  28   99  0.68

ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26


Consensus pattern (28 bp):   
CGCACACTTAGTGCTACATAATCAAACT

Found at i:3929 original size:83 final size:83

Alignment explanation


    Indices: 3730--3910  Score: 301
    Period size: 83  Copynumber: 2.2  Consensus size: 83

       3720 ATATTAAGTC

                    *       *            * *            *                    
       3730 CGCACACTCAGTGCTATATAATC-AACTCACACACTTAGTGCTATATAATCAAACTCGCACACTT
          1 CGCACACTTAGTGCTACATAATCAAACTCGCGCACTTAGTGCTACATAATCAAACTCGCACACTT

                              
       3794 ATGCTACATAATCAAACT
         66 ATGCTACATAATCAAACT

                                                                             
       3812 CGCACACTTAGTGCTACATAATCAAACTCGCGCACTTAGTGCTACATAATCAAACTCGCACACTT
          1 CGCACACTTAGTGCTACATAATCAAACTCGCGCACTTAGTGCTACATAATCAAACTCGCACACTT

                               
       3877 AGTGCTACATAATCAAACT
         66 A-TGCTACATAATCAAACT

                           
       3896 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       3911 GTACAATTTA


Statistics
Matches: 92,  Mismatches: 5, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  82   21  0.23
  83   39  0.42
  84   32  0.35

ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26


Consensus pattern (83 bp):   
CGCACACTTAGTGCTACATAATCAAACTCGCGCACTTAGTGCTACATAATCAAACTCGCACACTT
ATGCTACATAATCAAACT
Done.