Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold504

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: 29663
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:7671 original size:19 final size:19

Alignment explanation


    Indices: 7649--7686  Score: 60
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       7639 TCCTAATATT

                                
       7649 TAATATATTT-ATAATTTTA
          1 TAATAT-TTTAATAATTTTA

                               
       7668 TAATATTTTAATAATTTTA
          1 TAATATTTTAATAATTTTA

       7687 AAAAATTAGA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  18    3  0.17
  19   15  0.83

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (19 bp):   
TAATATTTTAATAATTTTA

Found at i:13692 original size:48 final size:46

Alignment explanation


    Indices: 13623--13742  Score: 159
    Period size: 46  Copynumber: 2.6  Consensus size: 46

      13613 TGTCTTCGAC

                         ** *              *                
      13623 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATCTAAT
          1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--ATATATCTAAT

                *                  *                      
      13671 ATGGGCTTACATGGCTCATTCCTATCTCCAAAGCCATATATCTAAT
          1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATCTAAT

                                *     
      13717 ATGGACTTACATGGCTCATTTCTGTC
          1 ATGGACTTACATGGCTCATTCCTGTC

      13743 CTGTCCTGTC


Statistics
Matches: 63,  Mismatches: 9, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  46   34  0.54
  48   29  0.46

ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36


Consensus pattern (46 bp):   
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATCTAAT

Found at i:20811 original size:46 final size:47

Alignment explanation


    Indices: 20705--20826  Score: 147
    Period size: 46  Copynumber: 2.6  Consensus size: 47

      20695 TGTCTTCGAC

                         ** *              *                  
      20705 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
          1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT

                *                                       *  
      20755 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
          1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT

                                *     
      20801 ATGGACTTACATGGCTCATTTCTGTC
          1 ATGGACTTACATGGCTCATTCCTGTC

      20827 CTGTCCTGTC


Statistics
Matches: 64,  Mismatches: 8, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  46   34  0.53
  50   30  0.47

ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36


Consensus pattern (47 bp):   
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Done.