Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1449

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: 35286
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1623 original size:41 final size:40

Alignment explanation


    Indices: 1539--1743  Score: 247
    Period size: 39  Copynumber: 5.1  Consensus size: 40

       1529 TTGGATTTAA

                                * *               *    
       1539 CCGGATATAGCT-ACTCGCTTCGAATGCCTTCGCGGACATAGC
          1 CCGGATATAG-TAACTCGC-ACAAATGCCTTCG-GGACTTAGC

                  *                                  
       1581 CCGGATGTAGTAACTCGCACAAATGCCTTCGGGACTTAAGC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTT-AGC

                                                   * 
       1622 CCGGATATTA-TAACTCGCACAAATGCCTTC-GGACTTAAC
          1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                                                    
       1661 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                  *    *   *  *            *        
       1701 CCGGA-CTAGTCACTAGCGCAAATGCCTTCGAGACTTAGC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                
       1740 CCGG
          1 CCGG

       1744 TTATCATCCG


Statistics
Matches: 146,  Mismatches: 12, Indels: 13
        0.85            0.07        0.08

Matches are distributed among these distances:
  38    2  0.01
  39   62  0.42
  40   24  0.16
  41   41  0.28
  42   17  0.12

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


Consensus pattern (40 bp):   
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

Found at i:12386 original size:20 final size:19

Alignment explanation


    Indices: 12350--12400  Score: 54
    Period size: 20  Copynumber: 2.7  Consensus size: 19

      12340 AAGGGCTATT

                         *      
      12350 TTGTAAA-GTTGTAAAATAA
          1 TTGTAAATG-TGTGAAATAA

                                
      12369 GTTGTAAATGTGTGAAATAA
          1 -TTGTAAATGTGTGAAATAA

                          
      12389 TTG-AAAT-TGTGA
          1 TTGTAAATGTGTGA

      12401 GTTGCTATAG


Statistics
Matches: 29,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  17    5  0.17
  18    4  0.14
  19    3  0.10
  20   16  0.55
  21    1  0.03

ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37


Consensus pattern (19 bp):   
TTGTAAATGTGTGAAATAA

Found at i:12926 original size:44 final size:45

Alignment explanation


    Indices: 12846--13066  Score: 223
    Period size: 45  Copynumber: 5.0  Consensus size: 45

      12836 TGATATTAAG

                         **      *                *      
      12846 TGATATATGTGAAAAATCCGAACTTGTTGAGTTGGTCCAAGTTCA
          1 TGATATATGTGAAGCATCCGAGCTTGTTGAGTTGGTCCGAGTTCA

                              *                  *       
      12891 TGATATATGTGAAGCATCTGAGC-TGTTGAGTTGGTCTGAGTTCA
          1 TGATATATGTGAAGCATCCGAGCTTGTTGAGTTGGTCCGAGTTCA

             *  **   *             **                   *
      12935 TTATCGATGCG-AGCATCCGAGCACGTTGAGTTGGTCCGAGTTCG
          1 TGATATATGTGAAGCATCCGAGCTTGTTGAGTTGGTCCGAGTTCA

                           *   *  *            *   *     *
      12979 TGATATATGTG-AGAAATCTGAACTTGTTGAGTTGTTCCAAGTTCG
          1 TGATATATGTGAAG-CATCCGAGCTTGTTGAGTTGGTCCGAGTTCA

                   *                *                  
      13024 TGATATAAGTGAAGCATCCGAGCTCGTTGAGTTGGTCCGAGTT
          1 TGATATATGTGAAGCATCCGAGCTTGTTGAGTTGGTCCGAGTT

      13067 TATTATGGAT


Statistics
Matches: 141,  Mismatches: 32, Indels: 6
        0.79            0.18        0.03

Matches are distributed among these distances:
  43   10  0.07
  44   53  0.38
  45   76  0.54
  46    2  0.01

ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33


Consensus pattern (45 bp):   
TGATATATGTGAAGCATCCGAGCTTGTTGAGTTGGTCCGAGTTCA

Found at i:19452 original size:30 final size:30

Alignment explanation


    Indices: 19417--19477  Score: 104
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      19407 TTGGAGAGTT

                   *                      
      19417 ACTTAAATAGATGGTCTTTAGTGTATAACC
          1 ACTTAAACAGATGGTCTTTAGTGTATAACC

                  *                       
      19447 ACTTAACCAGATGGTCTTTAGTGTATAACC
          1 ACTTAAACAGATGGTCTTTAGTGTATAACC

             
      19477 A
          1 A

      19478 TGAACTCAAC


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Consensus pattern (30 bp):   
ACTTAAACAGATGGTCTTTAGTGTATAACC
Done.