Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_2051

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: 25660
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:774 original size:29 final size:30

Alignment explanation


    Indices: 721--778  Score: 91
    Period size: 29  Copynumber: 2.0  Consensus size: 30

        711 TTTTGAAAAC

                             * *          
        721 ATTTACAAAAAGAGGCATCTAATTTTTAAT
          1 ATTTACAAAAAGAGGCACCAAATTTTTAAT

                                         
        751 ATTTACAAAAAGA-GCACCAAATTTTTAA
          1 ATTTACAAAAAGAGGCACCAAATTTTTAA

        779 AAATAATTCA


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  29   13  0.50
  30   13  0.50

ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33


Consensus pattern (30 bp):   
ATTTACAAAAAGAGGCACCAAATTTTTAAT

Found at i:3602 original size:28 final size:28

Alignment explanation


    Indices: 3562--3715  Score: 274
    Period size: 28  Copynumber: 5.5  Consensus size: 28

       3552 TAAATTGTAC

                                        
       3562 AGCACTAAGTGTGCGAGTTTGATTATGT
          1 AGCACTAAGTGTGCGAGTTTGATTATGT

                                        
       3590 AGCACTAAGTGTGCGAGTTTGATTATGT
          1 AGCACTAAGTGTGCGAGTTTGATTATGT

                                        
       3618 AGCACTAAGTGTGCGAGTTTGATTATGT
          1 AGCACTAAGTGTGCGAGTTTGATTATGT

                                   *    
       3646 AGCACTAAGTGTGCGAGTTTGATCATGT
          1 AGCACTAAGTGTGCGAGTTTGATTATGT

                                      * 
       3674 AGCACTAAGTGTGCGAG-TTGATTATAT
          1 AGCACTAAGTGTGCGAGTTTGATTATGT

                  *        
       3701 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

       3716 GACTTAATAT


Statistics
Matches: 122,  Mismatches: 4, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  27   22  0.18
  28  100  0.82

ACGTcount: A:0.25, C:0.12, G:0.29, T:0.33


Consensus pattern (28 bp):   
AGCACTAAGTGTGCGAGTTTGATTATGT

Found at i:11592 original size:28 final size:28

Alignment explanation


    Indices: 11552--11705  Score: 274
    Period size: 28  Copynumber: 5.5  Consensus size: 28

      11542 TAAATTGTAC

                                        
      11552 AGCACTAAGTGTGCGAGTTTGATTATGT
          1 AGCACTAAGTGTGCGAGTTTGATTATGT

                                        
      11580 AGCACTAAGTGTGCGAGTTTGATTATGT
          1 AGCACTAAGTGTGCGAGTTTGATTATGT

                                        
      11608 AGCACTAAGTGTGCGAGTTTGATTATGT
          1 AGCACTAAGTGTGCGAGTTTGATTATGT

                                      * 
      11636 AGCACTAAGTGTGCGAGTTTGATTATAT
          1 AGCACTAAGTGTGCGAGTTTGATTATGT

                                      * 
      11664 AGCACTAAGTGTGCGAG-TTGATTATAT
          1 AGCACTAAGTGTGCGAGTTTGATTATGT

                  *        
      11691 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

      11706 GACTTAATAT


Statistics
Matches: 124,  Mismatches: 2, Indels: 1
        0.98            0.02        0.01

Matches are distributed among these distances:
  27   24  0.19
  28  100  0.81

ACGTcount: A:0.26, C:0.12, G:0.29, T:0.34


Consensus pattern (28 bp):   
AGCACTAAGTGTGCGAGTTTGATTATGT

Found at i:11618 original size:56 final size:56

Alignment explanation


    Indices: 11527--11705  Score: 279
    Period size: 56  Copynumber: 3.2  Consensus size: 56

      11517 GAGATTGGCG

                       *     *   *  *                                
      11527 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
          1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA

                                  *                                 
      11584 CTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA

                                                              *     
      11640 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA

              *        
      11695 CTGAGTGTGCG
          1 CTAAGTGTGCG

      11706 GACTTAATAT


Statistics
Matches: 114,  Mismatches: 8, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
  55   23  0.20
  56   76  0.67
  57   15  0.13

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


Consensus pattern (56 bp):   
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA

Found at i:20578 original size:40 final size:40

Alignment explanation


    Indices: 20504--20685  Score: 253
    Period size: 40  Copynumber: 4.6  Consensus size: 40

      20494 AACCCAAGTA

                     *                     *         
      20504 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG

                    *                             * 
      20543 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
          1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG

                                    *               
      20583 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG

                                         *     *     
      20623 CCTTCGGGACTTAGCCCGGATATTA-TCACTAGCATAAATG
          1 CCTTCGGGACTTAGCCCGGATA-TAGTCAATAGCACAAATG

                         *         
      20663 CCTTCGGGACTTAACCCGGATAT
          1 CCTTCGGGACTTAGCCCGGATAT

      20686 CATTCGAATA


Statistics
Matches: 130,  Mismatches: 10, Indels: 6
        0.89            0.07        0.04

Matches are distributed among these distances:
  39   13  0.10
  40  112  0.86
  41    5  0.04

ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24


Consensus pattern (40 bp):   
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG

Done.