Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1996

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: 14283
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29


Found at i:1775 original size:31 final size:31

Alignment explanation


    Indices: 1718--1778  Score: 79
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       1708 CTCGCTGCAA

                     * *                   
       1718 TCTGGTGGCTTCGCCACATATATATATCTGT
          1 TCTGGTGGCCTAGCCACATATATATATCTGT

                                  *        
       1749 TCTGGTGGCCTAG-CACAATATCTATATCTG
          1 TCTGGTGGCCTAGCCAC-ATATATATATCTG

       1779 GTGACTTGTC


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  30    3  0.12
  31   23  0.88

ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36


Consensus pattern (31 bp):   
TCTGGTGGCCTAGCCACATATATATATCTGT

Found at i:8835 original size:27 final size:26

Alignment explanation


    Indices: 8791--8842  Score: 68
    Period size: 27  Copynumber: 2.0  Consensus size: 26

       8781 CTCGCTGCAA

                   *                   
       8791 TCTGGTGGCCTCGCCACATATATCTGT
          1 TCTGGTGACCTCGCCACA-ATATCTGT

                     *   *           
       8818 TCTGGTGACTTCGTCACAATATCTG
          1 TCTGGTGACCTCGCCACAATATCTG

       8843 GCAGCCTCGC


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  26    7  0.32
  27   15  0.68

ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35


Consensus pattern (26 bp):   
TCTGGTGACCTCGCCACAATATCTGT

Found at i:8918 original size:27 final size:26

Alignment explanation


    Indices: 8881--8939  Score: 66
    Period size: 27  Copynumber: 2.3  Consensus size: 26

       8871 CCACATATAT

                           *          
       8881 ATAT-TGTTCTGGTGGCCTAGCCACA
          1 ATATCTGTTCTGGTGACCTAGCCACA

                              * * *    
       8906 ATATCTGTATCTGGTGACTTCGTCACA
          1 ATATCTGT-TCTGGTGACCTAGCCACA

                   
       8933 ATATCTG
          1 ATATCTG

       8940 GCAGCCTCGC


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  25    4  0.14
  26    3  0.11
  27   21  0.75

ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36


Consensus pattern (26 bp):   
ATATCTGTTCTGGTGACCTAGCCACA
Done.