Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2621

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: 43288
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:2940 original size:46 final size:46

Alignment explanation


    Indices: 2873--3049  Score: 284
    Period size: 46  Copynumber: 3.8  Consensus size: 46

       2863 AGTGTGGAAT

                                                          
       2873 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
          1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA

                     *  *                              *  
       2919 GTAGGTATGATAGTTCAGTAAAGAAAACCATACTGAGTTGTGAGAA
          1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA

                             *          *                  
       2965 GTAGGTATGGTATTTCAATAACA-AAAATCATACTGAGTTGTGAAAA
          1 GTAGGTATGGTATTTCAGTAA-AGAAAACCATACTGAGTTGTGAAAA

                               *                   
       3011 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTT
          1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT

       3050 ATAGCATTGT


Statistics
Matches: 118,  Mismatches: 11, Indels: 4
        0.89            0.08        0.03

Matches are distributed among these distances:
  45    1  0.01
  46  116  0.98
  47    1  0.01

ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29


Consensus pattern (46 bp):   
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA

Found at i:4819 original size:43 final size:43

Alignment explanation


    Indices: 4772--4857  Score: 100
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       4762 TTGACTTTTT

                            ** *          *            
       4772 TTTTTGTATATATATATCATATATATTGACTTTTTTTTGTTAA
          1 TTTTTGTATATATATAAAACATATATTGACATTTTTTTGTTAA

                 * *              * *                  
       4815 TTTTTTTGTATATATAAAACATGTGTTGACATTTTTTTGTTAA
          1 TTTTTGTATATATATAAAACATATATTGACATTTTTTTGTTAA

       4858 GTTTATTTTT


Statistics
Matches: 35,  Mismatches: 8, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  43   35  1.00

ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58


Consensus pattern (43 bp):   
TTTTTGTATATATATAAAACATATATTGACATTTTTTTGTTAA
Done.