Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018206.1 Corchorus olitorius cultivar O-4 contig18239, whole genome shotgun sequence

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: 4874
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:1722 original size:27 final size:28

Alignment explanation


    Indices: 1668--1794  Score: 170
    Period size: 27  Copynumber: 4.6  Consensus size: 28

       1658 AAGTGAACTT

                               *        
       1668 AAAATGACCAAAATGCCCCCGGACATGC
          1 AAAATGACCAAAATGCCCCTGGACATGC

                                        
       1696 AAAATGACCAAAATGCCCC-GGACATGC
          1 AAAATGACCAAAATGCCCCTGGACATGC

                   *      *         *   
       1723 AAAATGAACAAAATACCCCTGGACGTGC
          1 AAAATGACCAAAATGCCCCTGGACATGC

                    *            *      
       1751 -AAATGACTAAAATGCCCCTGAACATGC
          1 AAAATGACCAAAATGCCCCTGGACATGC

                    *         
       1778 AAAA-GACTAAAATGCCC
          1 AAAATGACCAAAATGCCC

       1795 ACCTAGGTGA


Statistics
Matches: 89,  Mismatches: 8, Indels: 5
        0.87            0.08        0.05

Matches are distributed among these distances:
  27   60  0.67
  28   29  0.33

ACGTcount: A:0.43, C:0.28, G:0.17, T:0.13


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTGGACATGC

Found at i:1735 original size:55 final size:55

Alignment explanation


    Indices: 1668--1794  Score: 161
    Period size: 55  Copynumber: 2.3  Consensus size: 55

       1658 AAGTGAACTT

                   *                                         *      
       1668 AAAATGACCAAAATGCCCCCGGACATGCAAAATGACCAAAATGCCCC-GGACATGC
          1 AAAATGAACAAAATGCCCCCGGACATGC-AAATGACCAAAATGCCCCTGAACATGC

                          *    *    *          *                   
       1723 AAAATGAACAAAATACCCCTGGACGTGCAAATGACTAAAATGCCCCTGAACATGC
          1 AAAATGAACAAAATGCCCCCGGACATGCAAATGACCAAAATGCCCCTGAACATGC

                               
       1778 AAAA-G-ACTAAAATGCCC
          1 AAAATGAAC-AAAATGCCC

       1795 ACCTAGGTGA


Statistics
Matches: 63,  Mismatches: 7, Indels: 5
        0.84            0.09        0.07

Matches are distributed among these distances:
  53    2  0.03
  54   26  0.41
  55   35  0.56

ACGTcount: A:0.43, C:0.28, G:0.17, T:0.13


Consensus pattern (55 bp):   
AAAATGAACAAAATGCCCCCGGACATGCAAATGACCAAAATGCCCCTGAACATGC
Done.