Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold10653.1

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: 3396
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35


Found at i:2762 original size:12 final size:12

Alignment explanation


    Indices: 2746--2818  Score: 74
    Period size: 12  Copynumber: 5.8  Consensus size: 12

       2736 TTTTTGCTCG

                        
       2746 ATTTTTTTTTCA
          1 ATTTTTTTTTCA

            *         * 
       2758 CTTTTTTTTTGA
          1 ATTTTTTTTTCA

                           
       2770 ATTTTTTTTCAATCA
          1 ATTTTTTTT---TCA

                         
       2785 ATTTTTTTTTCGA
          1 ATTTTTTTTTC-A

                      **
       2798 ATTTTTTTTTTG
          1 ATTTTTTTTTCA

                     
       2810 ATTTTTTTT
          1 ATTTTTTTT

       2819 GTTACTCCAA


Statistics
Matches: 51,  Mismatches: 6, Indels: 8
        0.78            0.09        0.12

Matches are distributed among these distances:
  12   29  0.57
  13   11  0.22
  15   11  0.22

ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74


Consensus pattern (12 bp):   
ATTTTTTTTTCA

Found at i:2775 original size:13 final size:13

Alignment explanation


    Indices: 2759--2818  Score: 68
    Period size: 13  Copynumber: 4.5  Consensus size: 13

       2749 TTTTTTTCAC

                         
       2759 TTTTTTTTTGAAT
          1 TTTTTTTTTGAAT

                     * *   
       2772 TTTTTTTCAATCAAT
          1 TTTTTTT--TTGAAT

                    *    
       2787 TTTTTTTTCGAAT
          1 TTTTTTTTTGAAT

                         
       2800 TTTTTTTTTG-AT
          1 TTTTTTTTTGAAT

                   
       2812 TTTTTTT
          1 TTTTTTT

       2819 GTTACTCCAA


Statistics
Matches: 39,  Mismatches: 6, Indels: 5
        0.78            0.12        0.10

Matches are distributed among these distances:
  12    9  0.23
  13   19  0.49
  15   11  0.28

ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75


Consensus pattern (13 bp):   
TTTTTTTTTGAAT
Done.