Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2651

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: 2704
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:96 original size:16 final size:16

Alignment explanation


    Indices: 71--121  Score: 84
    Period size: 16  Copynumber: 3.2  Consensus size: 16

         61 AAGAAAGAGC

                            
         71 AAATACGCTAGTAAAT
          1 AAATACGCTAGTAAAT

            *    *          
         87 GAATATGCTAGTAAAT
          1 AAATACGCTAGTAAAT

                            
        103 AAATACGCTAGTAAAT
          1 AAATACGCTAGTAAAT

               
        119 AAA
          1 AAA

        122 ATACTAGAAA


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   31  1.00

ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25


Consensus pattern (16 bp):   
AAATACGCTAGTAAAT

Found at i:139 original size:32 final size:32

Alignment explanation


    Indices: 71--136  Score: 89
    Period size: 32  Copynumber: 2.1  Consensus size: 32

         61 AAGAAAGAGC

                               *  *    *   *
         71 AAATACGCTAGTAAATGAATATGCTAGTAAAT
          1 AAATACGCTAGTAAATGAAAATACTAGAAAAA

                                            
        103 AAATACGCTAGTAAAT-AAAATACTAGAAAAA
          1 AAATACGCTAGTAAATGAAAATACTAGAAAAA

               
        134 AAA
          1 AAA

        137 ATAGGCTTTC


Statistics
Matches: 30,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  31   14  0.47
  32   16  0.53

ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23


Consensus pattern (32 bp):   
AAATACGCTAGTAAATGAAAATACTAGAAAAA

Found at i:1732 original size:15 final size:15

Alignment explanation


    Indices: 1714--1744  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1704 ATAACTAAAG

                           
       1714 AAAAAATAGATAGAT
          1 AAAAAATAGATAGAT

                           
       1729 AAAAAATAGATAGAT
          1 AAAAAATAGATAGAT

             
       1744 A
          1 A

       1745 GATGAGAGAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19


Consensus pattern (15 bp):   
AAAAAATAGATAGAT
Done.