Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3587

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: 28171
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31


Found at i:2086 original size:40 final size:40

Alignment explanation


    Indices: 1985--2167  Score: 248
    Period size: 40  Copynumber: 4.5  Consensus size: 40

       1975 TATTCGGATG

                                                       
       1985 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC---TAGTTGCT

                                                     
       2028 ATA-CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTG-CT

                                       **            
       2067 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAG-TGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTG-CT

                          *                 *       
       2107 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGCT

                         *        
       2147 ATATCC-GGCTAAATCCCGAAG
          1 ATATCCGGGCTAAGTCCCGAAG

       2168 ATACTTGGGT


Statistics
Matches: 129,  Mismatches: 8, Indels: 10
        0.88            0.05        0.07

Matches are distributed among these distances:
  38    2  0.02
  39   21  0.16
  40   73  0.57
  41    2  0.02
  42   28  0.22
  43    3  0.02

ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25


Consensus pattern (40 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGCT

Found at i:10142 original size:40 final size:40

Alignment explanation


    Indices: 10105--10329  Score: 262
    Period size: 40  Copynumber: 5.7  Consensus size: 40

      10095 GCTACTCGTT

                            *  *                     
      10105 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA

                                                    
      10145 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                                    
      10185 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                **     *           * 
      10225 CAAATGCCTTC-GGATCTTAGTCC-GAATTAGTAACTCGTA
          1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA

                                **      * *  *    *   
      10264 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA

                               *      
      10305 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAACCCGGA

      10330 CATCATTCAA


Statistics
Matches: 167,  Mismatches: 13, Indels: 10
        0.88            0.07        0.05

Matches are distributed among these distances:
  39   40  0.24
  40  115  0.69
  41   12  0.07

ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

Found at i:15638 original size:28 final size:28

Alignment explanation


    Indices: 15573--15723  Score: 232
    Period size: 28  Copynumber: 5.4  Consensus size: 28

      15563 GAGATTGGCG

                       *     *   *  *    
      15573 CTAAGTGTGCGGGTTTAAATTGTACAGCA
          1 CTAAGTGTGCGAGTTT-GATTATATAGCA

                                  *     
      15602 CTAAGTGTGCGAGTTTGATTATGTAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                        
      15630 CTAAGTGTGCGAGTTTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                        
      15658 CTAAGTGTGCGAGTTTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                        
      15686 CTAAGTGTGCGAG-TTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

              *        
      15713 CTGAGTGTGCG
          1 CTAAGTGTGCG

      15724 GACTTAATAT


Statistics
Matches: 115,  Mismatches: 7, Indels: 2
        0.93            0.06        0.02

Matches are distributed among these distances:
  27   24  0.21
  28   76  0.66
  29   15  0.13

ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34


Consensus pattern (28 bp):   
CTAAGTGTGCGAGTTTGATTATATAGCA

Found at i:24018 original size:27 final size:28

Alignment explanation


    Indices: 23909--24058  Score: 223
    Period size: 27  Copynumber: 5.4  Consensus size: 28

      23899 GAGATTGGCG

                       *     *   *  *    
      23909 CTAAGTGTGCGGGTTTAAATTGTACAGCA
          1 CTAAGTGTGCGAGTTT-GATTATATAGCA

                                  *     
      23938 CTAAGTGTGCGAGTTTGATTATGTAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                        
      23966 CTAAGTGTGCGAGTTTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                        
      23994 CTAAGTGTGCGAG-TTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                        
      24021 CTAAGTGTGCGAG-TTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

              *        
      24048 CTGAGTGTGCG
          1 CTAAGTGTGCG

      24059 GACTTAATAT


Statistics
Matches: 114,  Mismatches: 7, Indels: 2
        0.93            0.06        0.02

Matches are distributed among these distances:
  27   51  0.45
  28   48  0.42
  29   15  0.13

ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33


Consensus pattern (28 bp):   
CTAAGTGTGCGAGTTTGATTATATAGCA

Found at i:24026 original size:55 final size:56

Alignment explanation


    Indices: 23909--24058  Score: 223
    Period size: 55  Copynumber: 2.7  Consensus size: 56

      23899 GAGATTGGCG

                       *     *   *  *                          *     
      23909 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
          1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCA

                                                                    
      23966 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCA

                                          *        
      24021 CTAAGTGTGCGAG-TTGATTATATAGCACTGAGTGTGCG
          1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCG

      24059 GACTTAATAT


Statistics
Matches: 87,  Mismatches: 6, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  54   24  0.28
  55   26  0.30
  56   22  0.25
  57   15  0.17

ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33


Consensus pattern (56 bp):   
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCA

Done.