Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1241

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: 5248
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:43 original size:14 final size:14

Alignment explanation


    Indices: 20--63  Score: 52
    Period size: 14  Copynumber: 3.1  Consensus size: 14

         10 TAGAAAAGAG

                 *     *  
         20 GGGTACGAATGGAA
          1 GGGTAGGAATGAAA

            *             
         34 TGGTAGGAATGAAA
          1 GGGTAGGAATGAAA

                      *   
         48 GGGTAGGAATAAAA
          1 GGGTAGGAATGAAA

              
         62 GG
          1 GG

         64 ATATGAACAA


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  14   25  1.00

ACGTcount: A:0.41, C:0.02, G:0.41, T:0.16


Consensus pattern (14 bp):   
GGGTAGGAATGAAA

Found at i:1839 original size:19 final size:20

Alignment explanation


    Indices: 1806--1846  Score: 75
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       1796 ACGAGAAGTT

                                
       1806 TGTTCGAATTTGTAGATAGA
          1 TGTTCGAATTTGTAGATAGA

                                
       1826 TGTTCGAA-TTGTAGATAGA
          1 TGTTCGAATTTGTAGATAGA

              
       1845 TG
          1 TG

       1847 AGTTAGATGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   13  0.62
  20    8  0.38

ACGTcount: A:0.29, C:0.05, G:0.27, T:0.39


Consensus pattern (20 bp):   
TGTTCGAATTTGTAGATAGA

Found at i:3080 original size:20 final size:20

Alignment explanation


    Indices: 3057--3103  Score: 58
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       3047 GGGTTAAGAT

                            *   
       3057 TGAGCTGAATTGAGCTTGAA
          1 TGAGCTGAATTGAGCTCGAA

                *   *          *
       3077 TGAGTTGACTTGAGCTCGAG
          1 TGAGCTGAATTGAGCTCGAA

                   
       3097 TGAGCTG
          1 TGAGCTG

       3104 GAAACAAGCT


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30


Consensus pattern (20 bp):   
TGAGCTGAATTGAGCTCGAA
Done.