Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1816

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: 22931
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32


Found at i:1249 original size:19 final size:19

Alignment explanation


    Indices: 1059--1250  Score: 125
    Period size: 19  Copynumber: 10.1  Consensus size: 19

       1049 TTATCCGATG

                             * 
       1059 ATGCACTATGTGTGCCAAT
          1 ATGCACTATGTGTGCCAGT

                     *         
       1078 ATGCACTATATGTGCCAGT
          1 ATGCACTATGTGTGCCAGT

              *   *       *  * 
       1097 ATACACAATGTGTGTCAAT
          1 ATGCACTATGTGTGCCAGT

                   * *         
       1116 ATGCACTTTATGTGCCAGT
          1 ATGCACTATGTGTGCCAGT

                   * *      *  
       1135 ATGCACTTTCTGTGCCCGT
          1 ATGCACTATGTGTGCCAGT

                     *     *  *
       1154 ATGCACTATTTGTGCTAGC
          1 ATGCACTATGTGTGCCAGT

                   * *   * *   
       1173 ATGCACTTTATGTTCTAGT
          1 ATGCACTATGTGTGCCAGT

               ***           * 
       1192 ATGTGTTATGTGTGCCAAT
          1 ATGCACTATGTGTGCCAGT

              **      *    **   
       1211 ATTAAC-ATTTTGTGTTAGT
          1 ATGCACTA-TGTGTGCCAGT

                               
       1230 ATGCACTATGTGTGCCAGT
          1 ATGCACTATGTGTGCCAGT

              
       1249 AT
          1 AT

       1251 TGACTTTGAA


Statistics
Matches: 126,  Mismatches: 45, Indels: 4
        0.72            0.26        0.02

Matches are distributed among these distances:
  18    1  0.01
  19  124  0.98
  20    1  0.01

ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38


Consensus pattern (19 bp):   
ATGCACTATGTGTGCCAGT

Found at i:15283 original size:51 final size:50

Alignment explanation


    Indices: 15203--15400  Score: 175
    Period size: 51  Copynumber: 3.9  Consensus size: 50

      15193 TGCCTATAAA

                      *     *                                   
      15203 CACGTGTGTAATACTAAGTGCAGGCTACTACGTGTATCG-AGAGATAATGGT
          1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAG-GAT-ATGGT

               *                          *       *     * *    
      15254 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGAAGGCTTTGGT
          1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-TCGAAGGATATGGT

                                *  *       *  * *     *   *  * 
      15305 CACGTGTGTAGTACTATGTGTAGCCTACTACATGAACCAGAAAG-TTTGAT
          1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAAGGATATGGT

                                *  *   *             *    
      15355 CACGTGTGTAGTACTATGTGAAGTCTAATACGTGTATCGAATGATA
          1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAGGATA

      15401 ATAATTACAC


Statistics
Matches: 118,  Mismatches: 25, Indels: 9
        0.78            0.16        0.06

Matches are distributed among these distances:
  49    4  0.03
  50   38  0.32
  51   70  0.59
  52    4  0.03
  53    2  0.02

ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31


Consensus pattern (50 bp):   
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAGGATATGGT
Done.