Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold11346.1

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: 2893
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32


Found at i:314 original size:40 final size:39

Alignment explanation


    Indices: 270--385  Score: 160
    Period size: 40  Copynumber: 2.9  Consensus size: 39

        260 ACATGAGAAT

                                                    
        270 TGCTAGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCG
          1 TGCTAGTGATGTATCCGG-CTAAGTCCCGAAGAGCATTCG

                                     *              
        310 TGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCG
          1 TGCTAGTGATGTATCC-GGCTAAGTCCCGAAGAGCATTCG

                *   * *           *             
        350 TGCTGGTGTTATATCCGCGCTAGGTCCCGAAGAGCA
          1 TGCTAGTGATGTATCCG-GCTAAGTCCCGAAGAGCA

        386 ATCATGCTGG


Statistics
Matches: 68,  Mismatches: 6, Indels: 4
        0.87            0.08        0.05

Matches are distributed among these distances:
  39    1  0.01
  40   65  0.96
  41    2  0.03

ACGTcount: A:0.22, C:0.22, G:0.29, T:0.26


Consensus pattern (39 bp):   
TGCTAGTGATGTATCCGGCTAAGTCCCGAAGAGCATTCG

Found at i:394 original size:40 final size:40

Alignment explanation


    Indices: 270--398  Score: 152
    Period size: 40  Copynumber: 3.2  Consensus size: 40

        260 ACATGAGAAT

                *     *                              
        270 TGCTAGTGATGTATCCG-GACTAAGTCCCGAAGAGCATTCG
          1 TGCTGGTGATATATCCGCG-CTAAGTCCCGAAGAGCATTCG

                *     *      *       *              
        310 TGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCG
          1 TGCTGGTGATATATCCGCGCTAAGTCCCGAAGAGCATTCG

                    *             *             *  *
        350 TGCTGGTGTTATATCCGCGCTAGGTCCCGAAGAGCAATCA
          1 TGCTGGTGATATATCCGCGCTAAGTCCCGAAGAGCATTCG

                     
        390 TGCTGGTGA
          1 TGCTGGTGA

        399 CGTGTATTCG


Statistics
Matches: 78,  Mismatches: 10, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  40   77  0.99
  41    1  0.01

ACGTcount: A:0.22, C:0.22, G:0.29, T:0.26


Consensus pattern (40 bp):   
TGCTGGTGATATATCCGCGCTAAGTCCCGAAGAGCATTCG

Found at i:792 original size:21 final size:21

Alignment explanation


    Indices: 768--817  Score: 91
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        758 TCGATATGTG

                                 
        768 AGAATATGTAAGACCATATCT
          1 AGAATATGTAAGACCATATCT

                                 
        789 AGAATATGTAAGACCATATCT
          1 AGAATATGTAAGACCATATCT

              *     
        810 AGGATATG
          1 AGAATATG

        818 GCATTGTAAG


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28


Consensus pattern (21 bp):   
AGAATATGTAAGACCATATCT
Done.