Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1377

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: 26523
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30


Found at i:5912 original size:20 final size:20

Alignment explanation


    Indices: 5887--5927  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5877 AAAAACGTGA

                            *   
       5887 ATGGAGTTAACCTATATTGT
          1 ATGGAGTTAACCTATACTGT

                    *           
       5907 ATGGAGTTGACCTATACTGT
          1 ATGGAGTTAACCTATACTGT

             
       5927 A
          1 A

       5928 GTTTTAAAGT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37


Consensus pattern (20 bp):   
ATGGAGTTAACCTATACTGT

Found at i:19701 original size:20 final size:20

Alignment explanation


    Indices: 19676--19716  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      19666 AAAAACGTGA

                            *   
      19676 ATGGAGTTAACCTATATTGT
          1 ATGGAGTTAACCTATACTGT

                    *           
      19696 ATGGAGTTGACCTATACTGT
          1 ATGGAGTTAACCTATACTGT

             
      19716 A
          1 A

      19717 GTTTTAAAGT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37


Consensus pattern (20 bp):   
ATGGAGTTAACCTATACTGT

Found at i:26185 original size:23 final size:24

Alignment explanation


    Indices: 26144--26195  Score: 88
    Period size: 23  Copynumber: 2.2  Consensus size: 24

      26134 ATGTAACAAC

                 *                  
      26144 ATTAATTAAATATTTTTAATTATA
          1 ATTAAATAAATATTTTTAATTATA

                                    
      26168 ATTAAATAAA-ATTTTTAATTATA
          1 ATTAAATAAATATTTTTAATTATA

                 
      26191 ATTAA
          1 ATTAA

      26196 TTGAGATTTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  23   18  0.67
  24    9  0.33

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (24 bp):   
ATTAAATAAATATTTTTAATTATA

Done.