Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold959

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: 18070
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:780 original size:13 final size:13

Alignment explanation


    Indices: 762--792  Score: 53
    Period size: 13  Copynumber: 2.4  Consensus size: 13

        752 ATAAACCTTT

                        *
        762 TGTATCGATACAC
          1 TGTATCGATACAA

                         
        775 TGTATCGATACAA
          1 TGTATCGATACAA

                 
        788 TGTAT
          1 TGTAT

        793 TGACAGAGAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35


Consensus pattern (13 bp):   
TGTATCGATACAA

Found at i:7657 original size:33 final size:32

Alignment explanation


    Indices: 7610--7677  Score: 93
    Period size: 33  Copynumber: 2.1  Consensus size: 32

       7600 CGTTACAAGC

                                          *   
       7610 CAATGTATCAATACAT-TTGGTCATGTATCTATA
          1 CAATGTATCAATACATCTT-GT-ATGTATCGATA

                     *                      
       7643 CAATGTATCGATACATCTTGTATGTATCGATA
          1 CAATGTATCAATACATCTTGTATGTATCGATA

               
       7675 CAA
          1 CAA

       7678 ACAGTTAAGG


Statistics
Matches: 32,  Mismatches: 2, Indels: 3
        0.86            0.05        0.08

Matches are distributed among these distances:
  32   13  0.41
  33   17  0.53
  34    2  0.06

ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37


Consensus pattern (32 bp):   
CAATGTATCAATACATCTTGTATGTATCGATA

Found at i:9832 original size:51 final size:51

Alignment explanation


    Indices: 9756--9898  Score: 223
    Period size: 51  Copynumber: 2.8  Consensus size: 51

       9746 TATGGAAAGG

                            *                                  
       9756 TACCCAGATGTATCGAAACATTCTTCAATGTATCGATACATTCTATCCTTT
          1 TACCCAGATGTATCGATACATTCTTCAATGTATCGATACATTCTATCCTTT

                              *                         *  *   
       9807 TACCCAGATGTATCGATATATTCTTCAATGTATCGATACATTCTGTCTTTT
          1 TACCCAGATGTATCGATACATTCTTCAATGTATCGATACATTCTATCCTTT

                 *                *          *       
       9858 TACCCGGATGTATCGATACATTTTTCAATGTATTGATACAT
          1 TACCCAGATGTATCGATACATTCTTCAATGTATCGATACAT

       9899 CTAGTTAAAA


Statistics
Matches: 84,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  51   84  1.00

ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40


Consensus pattern (51 bp):   
TACCCAGATGTATCGATACATTCTTCAATGTATCGATACATTCTATCCTTT

Found at i:10874 original size:20 final size:20

Alignment explanation


    Indices: 10849--10898  Score: 66
    Period size: 20  Copynumber: 2.5  Consensus size: 20

      10839 CCCTTAAAAA

                                 
      10849 TATCGATACACAATT-CAAAG
          1 TATCGATACA-AATTGCAAAG

                      **        
      10869 TATCGATACATGTTGCAAAG
          1 TATCGATACAAATTGCAAAG

                      
      10889 TATCGATACA
          1 TATCGATACA

      10899 TGAAAAAAAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  19    2  0.07
  20   25  0.93

ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28


Consensus pattern (20 bp):   
TATCGATACAAATTGCAAAG
Done.