Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024531.1 Corchorus olitorius cultivar O-4 contig24564, 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: 23655
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:6552 original size:28 final size:28

Alignment explanation


    Indices: 6521--6590  Score: 131
    Period size: 28  Copynumber: 2.5  Consensus size: 28

       6511 AGTGCACTCG

                                        
       6521 AAATGACCAAAATGCCCCTGGAGATGAA
          1 AAATGACCAAAATGCCCCTGGAGATGAA

                   *                    
       6549 AAATGACAAAAATGCCCCTGGAGATGAA
          1 AAATGACCAAAATGCCCCTGGAGATGAA

                          
       6577 AAATGACCAAAATG
          1 AAATGACCAAAATG

       6591 AGAAGTAAAT


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  28   40  1.00

ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14


Consensus pattern (28 bp):   
AAATGACCAAAATGCCCCTGGAGATGAA

Found at i:7729 original size:22 final size:22

Alignment explanation


    Indices: 7698--7741  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       7688 TTCTTTCCGC

                       *          
       7698 AACAACTTCTGTCCCGAAGTTG
          1 AACAACTTCTGGCCCGAAGTTG

                 *      *         
       7720 AACAAGTTCTGGGCCGAAGTTG
          1 AACAACTTCTGGCCCGAAGTTG

       7742 TCCTGCAATT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25


Consensus pattern (22 bp):   
AACAACTTCTGGCCCGAAGTTG

Found at i:22627 original size:21 final size:21

Alignment explanation


    Indices: 22602--22642  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      22592 TTAGAAACCC

                                  
      22602 TAGTACCACTTAG-ATCCAATT
          1 TAGTACCACTT-GTATCCAATT

                                
      22623 TAGTACCACTTGTATCCAAT
          1 TAGTACCACTTGTATCCAAT

      22643 AGGGCTTCAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    1  0.05
  21   18  0.95

ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34


Consensus pattern (21 bp):   
TAGTACCACTTGTATCCAATT
Done.