Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold12867.1

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: 2033
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36


Found at i:847 original size:5 final size:5

Alignment explanation


    Indices: 832--888  Score: 78
    Period size: 5  Copynumber: 11.2  Consensus size: 5

        822 AGTGGAAAAG

                                                             *     *    
        832 TGAATT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT GGAAT GGAAT
          1 TGAA-T TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT

            *      
        883 GGAAT T
          1 TGAAT T

        889 ATGATTAATT


Statistics
Matches: 49,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
   5   45  0.92
   6    4  0.08

ACGTcount: A:0.39, C:0.00, G:0.25, T:0.37


Consensus pattern (5 bp):   
TGAAT

Found at i:1367 original size:45 final size:45

Alignment explanation


    Indices: 1303--1442  Score: 217
    Period size: 45  Copynumber: 3.1  Consensus size: 45

       1293 CTGCTACTGC

                     *            *      *               
       1303 TACTGCTACTGTTACCGATTCGGCACTTTATGTGTCGAATATTGT
          1 TACTGCTACCGTTACCGATTCGACACTTTGTGTGTCGAATATTGT

                                                         
       1348 TACTGCTACCGTTACCGATTCGACACTTTGTGTGTCGAATATTGT
          1 TACTGCTACCGTTACCGATTCGACACTTTGTGTGTCGAATATTGT

                 *               *             *     *   
       1393 TACTGTTACCGTTACCGATTCAACACTTTGTGTGTTGAATACTGT
          1 TACTGCTACCGTTACCGATTCGACACTTTGTGTGTCGAATATTGT

                 
       1438 TACTG
          1 TACTG

       1443 TTACTGTTCC


Statistics
Matches: 88,  Mismatches: 7, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  45   88  1.00

ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39


Consensus pattern (45 bp):   
TACTGCTACCGTTACCGATTCGACACTTTGTGTGTCGAATATTGT

Found at i:1647 original size:18 final size:18

Alignment explanation


    Indices: 1626--1896  Score: 140
    Period size: 18  Copynumber: 14.6  Consensus size: 18

       1616 TAACTGATTA

                              
       1626 TTACTGAATAATTGACTG
          1 TTACTGAATAATTGACTG

                * *           
       1644 TTACCGGATAATTGACTG
          1 TTACTGAATAATTGACTG

                  *            
       1662 TTACTGGAT-ATTAGACTG
          1 TTACTGAATAATT-GACTG

                       *   * *
       1680 TTACTGAATAACTGAATA
          1 TTACTGAATAATTGACTG

                              *
       1698 TTACTGAATAATTGA-TCA
          1 TTACTGAATAATTGACT-G

                       * * *  
       1716 TTACTGAATAACTAATTG
          1 TTACTGAATAATTGACTG

             *             *  *
       1734 TCACTGAATGAA-TGCCTA
          1 TTACTGAAT-AATTGACTG

            *             * *  
       1752 CTACTGAATAACTTAATTG
          1 TTACTGAATAA-TTGACTG

                            * *
       1771 TTACTGAAT-ATCT-AATT
          1 TTACTGAATAAT-TGACTG

                              
       1788 TTACTGAATAATTGACTG
          1 TTACTGAATAATTGACTG

                                       
       1806 TTACTGGATAACCGATCAATTGA-TCG
          1 TTACT-G---A---AT-AATTGACT-G

            *          *  ** *
       1832 ATACTGAATAACTGGTTA
          1 TTACTGAATAATTGACTG

               *              
       1850 TTATTGAATAATTGACTG
          1 TTACTGAATAATTGACTG

                *      *      
       1868 TTACCGAATAACTGACTG
          1 TTACTGAATAATTGACTG

                       
       1886 TTACTGAATAA
          1 TTACTGAATAA

       1897 ATAATTGTTC


Statistics
Matches: 192,  Mismatches: 41, Indels: 40
        0.70            0.15        0.15

Matches are distributed among these distances:
  17   19  0.10
  18  137  0.71
  19   19  0.10
  22    2  0.01
  25    4  0.02
  26   11  0.06

ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36


Consensus pattern (18 bp):   
TTACTGAATAATTGACTG

Done.