Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1860

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: 16012
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30


Found at i:3792 original size:18 final size:18

Alignment explanation


    Indices: 3769--3803  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3759 TATGCATTTT

                              
       3769 ATGTGACAGCCCAAAATC
          1 ATGTGACAGCCCAAAATC

                             
       3787 ATGTGACAGCCCAAAAT
          1 ATGTGACAGCCCAAAAT

       3804 TGACCCTAGC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17


Consensus pattern (18 bp):   
ATGTGACAGCCCAAAATC

Found at i:5619 original size:27 final size:27

Alignment explanation


    Indices: 5452--5629  Score: 119
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       5442 TAAATTGTAC

                                *        
       5452 AGCACTAAGTGTGCGA-TTCTACTT-TGT
          1 AGCACTAAGTGTGCGAGTT-GA-TTATGT

            *               **   *     
       5479 TGCACTAAGTGTGCGAAATGAATATG-
          1 AGCACTAAGTGTGCGAGTTGATTATGT

                      *      *    **  **
       5505 ATGCACTAAGAGTGCGAATTGACCATAC
          1 A-GCACTAAGTGTGCGAGTTGATTATGT

            *                   * *     
       5533 GGCACTAAGTGTGCGAGTCTAACTATGT
          1 AGCACTAAGTGTGCGAGT-TGATTATGT

                            *       *  
       5561 AGCACTAAGTGTGCGATTTGATTACGT
          1 AGCACTAAGTGTGCGAGTTGATTATGT

            *       *                * 
       5588 GGCACTAAATGTGCGAGTTGATTATAT
          1 AGCACTAAGTGTGCGAGTTGATTATGT

                  *        
       5615 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

       5630 GGCTCAATAT


Statistics
Matches: 116,  Mismatches: 30, Indels: 10
        0.74            0.19        0.06

Matches are distributed among these distances:
  26    1  0.01
  27   93  0.80
  28   22  0.19

ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29


Consensus pattern (27 bp):   
AGCACTAAGTGTGCGAGTTGATTATGT

Found at i:5620 original size:82 final size:81

Alignment explanation


    Indices: 5449--5629  Score: 204
    Period size: 82  Copynumber: 2.2  Consensus size: 81

       5439 GATTAAATTG

                               *      *   *                       *          
       5449 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
          1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA

                            
       5514 GAGTGCGAATTGACCA
         66 GAGTGCGAATTGACCA

               *                                           **   *            
       5530 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
          1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT

                       *    ** 
       5594 AA-ATGTGCGAGTTGATTA
         64 AAGA-GTGCGAATTGACCA

              *      *        
       5612 TATAGCACTGAGTGTGCG
          1 TACAGCACTAAGTGTGCG

       5630 GGCTCAATAT


Statistics
Matches: 83,  Mismatches: 14, Indels: 5
        0.81            0.14        0.05

Matches are distributed among these distances:
  81   23  0.28
  82   60  0.72

ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29


Consensus pattern (81 bp):   
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA

Found at i:13621 original size:27 final size:27

Alignment explanation


    Indices: 13454--13631  Score: 119
    Period size: 27  Copynumber: 6.6  Consensus size: 27

      13444 TAAATTGTAC

                                *        
      13454 AGCACTAAGTGTGCGA-TTCTACTT-TGT
          1 AGCACTAAGTGTGCGAGTT-GA-TTATGT

            *               **   *     
      13481 TGCACTAAGTGTGCGAAATGAATATG-
          1 AGCACTAAGTGTGCGAGTTGATTATGT

                      *      *    **  **
      13507 ATGCACTAAGAGTGCGAATTGACCATAC
          1 A-GCACTAAGTGTGCGAGTTGATTATGT

            *                   * *     
      13535 GGCACTAAGTGTGCGAGTCTAACTATGT
          1 AGCACTAAGTGTGCGAGT-TGATTATGT

                            *       *  
      13563 AGCACTAAGTGTGCGATTTGATTACGT
          1 AGCACTAAGTGTGCGAGTTGATTATGT

            *       *                * 
      13590 GGCACTAAATGTGCGAGTTGATTATAT
          1 AGCACTAAGTGTGCGAGTTGATTATGT

                  *        
      13617 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

      13632 GGCTCAATAT


Statistics
Matches: 116,  Mismatches: 30, Indels: 10
        0.74            0.19        0.06

Matches are distributed among these distances:
  26    1  0.01
  27   93  0.80
  28   22  0.19

ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29


Consensus pattern (27 bp):   
AGCACTAAGTGTGCGAGTTGATTATGT

Found at i:13622 original size:82 final size:81

Alignment explanation


    Indices: 13451--13631  Score: 204
    Period size: 82  Copynumber: 2.2  Consensus size: 81

      13441 GATTAAATTG

                               *      *   *                       *          
      13451 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
          1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA

                            
      13516 GAGTGCGAATTGACCA
         66 GAGTGCGAATTGACCA

               *                                           **   *            
      13532 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
          1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT

                       *    ** 
      13596 AA-ATGTGCGAGTTGATTA
         64 AAGA-GTGCGAATTGACCA

              *      *        
      13614 TATAGCACTGAGTGTGCG
          1 TACAGCACTAAGTGTGCG

      13632 GGCTCAATAT


Statistics
Matches: 83,  Mismatches: 14, Indels: 5
        0.81            0.14        0.05

Matches are distributed among these distances:
  81   23  0.28
  82   60  0.72

ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29


Consensus pattern (81 bp):   
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Done.